Variant report

Variant	rs1888138
Chromosome Location	chr13:91999496-91999497
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:91999153-92001929	H1-hESC	embryonic stem cell:	n/a	n/a
2	TCF7L2	chr13:91999245-92001683	HCT-116	colon:	n/a	n/a
3	ATF2	chr13:91999029-91999593	GM12878	blood:	n/a	n/a
4	MAZ	chr13:91998533-92004929	K562	blood:	n/a	chr13:91999821-91999831 chr13:91998551-91998561 chr13:92001061-92001071 chr13:92001123-92001132 chr13:92000750-92000759
5	POLR2A	chr13:91998902-92001951	GM19099	blood:	n/a	n/a
6	POLR2A	chr13:91999044-91999731	GM12878	blood:	n/a	n/a
7	KAP1	chr13:91998949-91999777	HEK293	kidney:	n/a	n/a
8	YY1	chr13:91999419-92000376	GM12891	blood:	n/a	chr13:91999968-91999977 chr13:91999966-91999980 chr13:91999963-91999977 chr13:91999766-91999780 chr13:92000222-92000236 chr13:91999763-91999777 chr13:91999971-91999980 chr13:91999765-91999774 chr13:91999818-91999832 chr13:91999922-91999936 chr13:91999968-91999979
9	POLR2A	chr13:91999396-92000234	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr13:91999484-91999774	HepG2	liver:	n/a	n/a
11	POLR2A	chr13:91998938-92001748	Raji	blood:	n/a	n/a
12	POLR2A	chr13:91998832-92013433	K562	blood:	n/a	n/a
13	TCF12	chr13:91999004-92000115	A549	lung:	n/a	n/a
14	POLR2A	chr13:91998968-92003731	K562	blood:	n/a	n/a
15	BCLAF1	chr13:91998654-92000393	K562	blood:	n/a	chr13:91999970-91999979 chr13:91999772-91999785 chr13:91999759-91999772 chr13:91999967-91999976 chr13:91999968-91999981 chr13:91999967-91999980 chr13:92000044-92000057 chr13:91999923-91999936
16	MAX	chr13:91999112-92000081	H1-hESC	embryonic stem cell:	n/a	chr13:91999821-91999831
17	BACH1	chr13:91998969-92000215	K562	blood:	n/a	n/a
18	ZNF143	chr13:91999244-92000141	H1-hESC	embryonic stem cell:	n/a	n/a
19	RELA	chr13:91998965-92000176	GM18951	blood:	n/a	chr13:91999115-91999124 chr13:91999115-91999124
20	GABPA	chr13:91999077-92000290	K562	blood:	n/a	chr13:91999848-91999857 chr13:91999624-91999633 chr13:91999821-91999830 chr13:91999637-91999651
21	ELF1	chr13:91999400-92000093	HepG2	liver:	n/a	chr13:92000048-92000057 chr13:91999670-91999679 chr13:91999968-91999977 chr13:91999971-91999980 chr13:91999967-91999979
22	CREB1	chr13:91998190-92005186	K562	blood:	n/a	n/a
23	CREB1	chr13:91999424-92000285	GM12878	blood:	n/a	n/a
24	GABPA	chr13:91999062-92001679	K562	blood:	n/a	chr13:91999848-91999857 chr13:92000697-92000706 chr13:92000739-92000748 chr13:91999624-91999633 chr13:91999821-91999830 chr13:91999637-91999651
25	MAZ	chr13:91999300-92001581	Hela-S3	cervix:	n/a	chr13:91999821-91999831 chr13:92001061-92001071 chr13:92001123-92001132 chr13:92000750-92000759
26	IRF1	chr13:91999051-92000236	K562	blood:	n/a	chr13:91999820-91999834 chr13:92000024-92000038 chr13:91999672-91999686
27	POLR2A	chr13:91999007-92004670	GM18951	blood:	n/a	n/a
28	TAF1	chr13:91999389-92001771	K562	blood:	n/a	n/a
29	POLR2A	chr13:91999055-92001790	GM12892	blood:	n/a	n/a
30	MXI1	chr13:91998376-92005054	K562	blood:	n/a	n/a
31	RELA	chr13:91997747-92000138	GM19193	blood:	n/a	chr13:91999115-91999124 chr13:91998500-91998509 chr13:91998500-91998509 chr13:91999115-91999124
32	TCF7L2	chr13:91999208-92000239	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr13:91999113-92002032	GM15510	blood:	n/a	n/a
34	POLR2A	chr13:91998860-92001773	GM19193	blood:	n/a	n/a
35	YY1	chr13:91999151-92001703	K562	blood:	n/a	chr13:91999968-91999977 chr13:92001025-92001047 chr13:92000669-92000680 chr13:92000666-92000677 chr13:91999966-91999980 chr13:91999963-91999977 chr13:92000863-92000877 chr13:92001025-92001035 chr13:91999766-91999780 chr13:92000799-92000808 chr13:92001021-92001030 chr13:92001138-92001149 chr13:92000222-92000236 chr13:92000668-92000677 chr13:92001142-92001153 chr13:91999763-91999777 chr13:92001022-92001042 chr13:91999971-91999980 chr13:92001601-92001612 chr13:92001089-92001098 chr13:91999765-91999774 chr13:91999818-91999832 chr13:92001320-92001329 chr13:92000671-92000680 chr13:91999922-91999936 chr13:91999968-91999979 chr13:92001381-92001395 chr13:92000668-92000682
36	TBL1XR1	chr13:91998914-92005070	K562	blood:	n/a	n/a
37	CHD2	chr13:91998857-92004937	K562	blood:	n/a	chr13:91999921-91999931 chr13:92000220-92000230 chr13:91999849-91999859 chr13:91999694-91999704 chr13:91999681-91999691
38	SP1	chr13:91999389-91999773	A549	lung:	n/a	chr13:91999673-91999683
39	RFX5	chr13:91999142-92000141	Hela-S3	cervix:	n/a	n/a
40	PML	chr13:91998755-92014623	K562	blood:	n/a	chr13:92004530-92004538
41	CCNT2	chr13:91999216-92001980	K562	blood:	n/a	chr13:92000025-92000034 chr13:92001155-92001164 chr13:92001601-92001610 chr13:92001181-92001190
42	TAF7	chr13:91999485-92000333	K562	blood:	n/a	n/a
43	YY1	chr13:91999209-92001745	K562	blood:	n/a	chr13:91999968-91999977 chr13:92001025-92001047 chr13:92000669-92000680 chr13:92000666-92000677 chr13:91999966-91999980 chr13:91999963-91999977 chr13:92000863-92000877 chr13:92001025-92001035 chr13:91999766-91999780 chr13:92000799-92000808 chr13:92001021-92001030 chr13:92001138-92001149 chr13:92000222-92000236 chr13:92000668-92000677 chr13:92001142-92001153 chr13:91999763-91999777 chr13:92001022-92001042 chr13:91999971-91999980 chr13:92001601-92001612 chr13:92001089-92001098 chr13:91999765-91999774 chr13:91999818-91999832 chr13:92001320-92001329 chr13:92000671-92000680 chr13:91999922-91999936 chr13:91999968-91999979 chr13:92001381-92001395 chr13:92000668-92000682
44	EBF1	chr13:91998961-92000064	GM12878	blood:	n/a	n/a
45	GTF2F1	chr13:91999273-91999538	Hela-S3	cervix:	n/a	n/a
46	MAZ	chr13:91999294-92000141	HepG2	liver:	n/a	chr13:91999821-91999831
47	SIN3AK20	chr13:91999384-92000316	PANC-1	pancreas:	n/a	n/a
48	ZNF143	chr13:91999411-92000087	GM12878	blood:	n/a	n/a
49	NR2F2	chr13:91998855-92000257	K562	blood:	n/a	n/a
50	CTCF	chr13:91999185-92001945	SK-N-SH	brain:	n/a	chr13:92001323-92001333 chr13:92001322-92001335 chr13:92001326-92001335 chr13:92001321-92001337 chr13:92001320-92001338 chr13:92000700-92000716 chr13:92001360-92001373 chr13:92000702-92000715 chr13:92001322-92001335 chr13:92000733-92000746 chr13:92000699-92000717

No.	Distal block	Cell Line	Cell type
1	chr13:91998556..92002777-chr9:134147037..134155728,18	K562	blood:
2	chr13:91999405..92003025-chr22:23522118..23524074,3	K562	blood:
3	chr1:33004093..33007091-chr13:91999311..92002195,5	K562	blood:
4	chr13:91998254..92002103-chr22:22898499..22902488,4	K562	blood:
5	chr1:33004072..33007091-chr13:91999311..92001675,4	K562	blood:
6	chr13:91998254..92001076-chr22:22898499..22901171,2	K562	blood:
7	chr12:49656589..49659420-chr13:91999028..92001178,2	K562	blood:
8	chr13:91998892..92001087-chrX:152952239..152954221,2	K562	blood:
9	chr13:91998556..92001592-chr9:134150017..134155728,10	K562	blood:
10	chr13:91999417..92000348-chr16:88922774..88923477,2	NB4	blood:
11	chr13:91999380..92000118-chr9:4679003..4679675,2	NB4	blood:
12	chr13:91899592..91901099-chr13:91998004..91999669,2	K562	blood:
13	chr13:91998294..91999880-chr13:92024685..92027354,2	MCF-7	breast:
14	chr13:91998776..92000555-chr13:92831916..92834550,2	K562	blood:
15	chr13:91998703..91999501-chr2:70314810..70315727,2	Hela-S3	cervix:
16	chr13:91922956..91924872-chr13:91999191..92001609,2	K562	blood:
17	chr13:91999220..92000207-chr19:59055377..59055970,2	HCT-116	colon:
18	chr1:167905256..167905963-chr13:91999310..92000299,2	Hela-S3	cervix:
19	chr13:91998997..92001437-chr21:34913809..34915620,2	K562	blood:
20	chr13:91996769..92000031-chr13:92330723..92334670,4	K562	blood:

Variant related genes	Relation type
MIR17HG	TF binding region
ENSG00000214178	Chromatin interaction
ENSG00000106993	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000220891	Chromatin interaction
ENSG00000159140	Chromatin interaction
ENSG00000143158	Chromatin interaction
ENSG00000179818	Chromatin interaction
ENSG00000141012	Chromatin interaction
ENSG00000236794	Chromatin interaction
ENSG00000186716	Chromatin interaction
ENSG00000143164	Chromatin interaction
ENSG00000229287	Chromatin interaction
ENSG00000130726	Chromatin interaction
ENSG00000160062	Chromatin interaction
ENSG00000130821	Chromatin interaction
ENSG00000130822	Chromatin interaction
ENSG00000126882	Chromatin interaction
ENSG00000273061	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000159131	Chromatin interaction
ENSG00000185686	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11838867	0.82[ASN][1000 genomes]
rs11839648	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11842349	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12583515	0.81[EUR][1000 genomes]
rs12583555	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17667894	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17667900	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17667931	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17667973	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17735357	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17735387	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17735544	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59829937	0.87[EUR][1000 genomes]
rs60279891	0.87[EUR][1000 genomes]
rs60699901	0.94[ASN][1000 genomes]
rs7323996	0.93[ASN][1000 genomes]
rs7324952	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042947	chr13:91571040-92416897	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
2	nsv541871	chr13:91571040-92416897	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
3	esv1803618	chr13:91669587-92277699	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1945 gene(s)	inside rSNPs	diseases
4	nsv1050259	chr13:91759549-92152078	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
5	nsv541872	chr13:91759549-92152078	Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
6	nsv832679	chr13:91859467-92030220	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1943 gene(s)	inside rSNPs	diseases
7	esv1794000	chr13:91983910-92001350	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
8	esv1797111	chr13:91983910-92001472	Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
9	nsv562694	chr13:91992157-92001119	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
10	esv1796195	chr13:91992157-92001472	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
11	esv1840145	chr13:91992157-92001472	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
12	nsv562695	chr13:91992157-92001472	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
13	esv1795019	chr13:91992157-92003589	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1146 gene(s)	inside rSNPs	diseases
14	esv3404637	chr13:91998776-92001324	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
15	esv3347426	chr13:91999026-92002299	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
16	esv3375166	chr13:91999176-92001724	Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:91998000-91999600	Flanking Active TSS	GM12878-XiMat	blood
2	chr13:91998600-91999600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr13:91998600-91999600	Flanking Active TSS	Dnd41	blood
4	chr13:91998600-91999800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr13:91998800-91999600	Flanking Active TSS	K562	blood
6	chr13:91998800-91999800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr13:91998800-91999800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr13:91999000-91999600	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr13:91999000-91999600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
10	chr13:91999000-91999600	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr13:91999000-91999600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr13:91999000-91999600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr13:91999000-91999600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
14	chr13:91999000-91999600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr13:91999000-91999600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr13:91999000-91999600	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr13:91999000-91999600	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr13:91999000-91999600	Flanking Active TSS	Fetal Intestine Large	intestine
19	chr13:91999000-91999600	Bivalent/Poised TSS	A549	lung
20	chr13:91999000-91999600	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
21	chr13:91999000-91999600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
22	chr13:91999000-91999600	Flanking Active TSS	NHEK	skin
23	chr13:91999000-91999800	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr13:91999000-91999800	Active TSS	Fetal Kidney	kidney
25	chr13:91999000-91999800	Flanking Active TSS	HMEC	breast
26	chr13:91999000-92001000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr13:91999000-92001400	Active TSS	Rectal Smooth Muscle	rectum
28	chr13:91999000-92001600	Active TSS	H1 Cell Line	embryonic stem cell
29	chr13:91999000-92001600	Active TSS	Brain Angular Gyrus	brain
30	chr13:91999000-92001600	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr13:91999000-92001800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr13:91999000-92001800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr13:91999000-92001800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr13:91999000-92001800	Active TSS	Brain Substantia Nigra	brain
35	chr13:91999000-92002200	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr13:91999000-92002200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr13:91999000-92002200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr13:91999000-92002200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr13:91999000-92002400	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr13:91999000-92002800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr13:91999000-92003000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr13:91999200-91999600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr13:91999200-91999600	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr13:91999200-91999600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr13:91999200-91999600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
46	chr13:91999200-91999600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
47	chr13:91999200-91999600	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr13:91999200-91999600	Flanking Active TSS	Primary B cells from peripheral blood	blood
49	chr13:91999200-91999600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr13:91999200-91999600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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