Variant report

Variant	rs943233
Chromosome Location	chr13:39612264-39612265
allele	A/G
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	MAX	chr13:39611904-39612741	K562	blood:	n/a	n/a
2	POLR2A	chr13:39611683-39612934	IMR90	lung:	n/a	n/a
3	ELF1	chr13:39611747-39612819	MCF-7	breast:	n/a	chr13:39612009-39612018
4	FOXA2	chr13:39611875-39612303	A549	lung:	n/a	n/a
5	FOXA1	chr13:39611971-39612270	T-47D	breast:	n/a	n/a
6	ETS1	chr13:39611702-39612275	K562	blood:	n/a	chr13:39611818-39611829
7	MYC	chr13:39611567-39612654	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAZ	chr13:39611844-39612590	HepG2	liver:	n/a	n/a
9	TFAP2A	chr13:39612045-39612901	Hela-S3	cervix:	n/a	chr13:39612483-39612498
10	STAT3	chr13:39611981-39612594	MCF10A-Er-Src	breast:	n/a	chr13:39612220-39612231
11	NFYB	chr13:39612066-39613071	GM12878	blood:	n/a	n/a
12	POLR2A	chr13:39611646-39612300	GM12878	blood:	n/a	n/a
13	E2F6	chr13:39612093-39612944	A549	lung:	n/a	chr13:39612491-39612502
14	SIN3A	chr13:39611702-39612983	GM12878	blood:	n/a	chr13:39611723-39611734
15	TEAD4	chr13:39612015-39612340	K562	blood:	n/a	n/a
16	CTCF	chr13:39611972-39612389	K562	blood:	n/a	chr13:39612038-39612051
17	ARID3A	chr13:39611899-39613084	HepG2	liver:	n/a	n/a
18	POLR2A	chr13:39611852-39612688	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr13:39611624-39613122	Raji	blood:	n/a	n/a
20	RUNX3	chr13:39611484-39613094	GM12878	blood:	n/a	n/a
21	SIN3AK20	chr13:39611725-39613195	MCF-7	breast:	n/a	n/a
22	USF1	chr13:39612215-39612633	A549	lung:	n/a	n/a
23	POLR2A	chr13:39611841-39612297	A549	lung:	n/a	n/a
24	TAF1	chr13:39611700-39612999	GM12878	blood:	n/a	n/a
25	SP1	chr13:39611877-39612648	H1-hESC	embryonic stem cell:	n/a	chr13:39612233-39612244
26	POLR2A	chr13:39611727-39612880	U87	brain:	n/a	n/a
27	FOXP2	chr13:39611750-39612274	PFSK-1	brain:	n/a	n/a
28	ARID3A	chr13:39612015-39612617	K562	blood:	n/a	n/a
29	POLR2A	chr13:39611629-39613070	MCF-7	breast:	n/a	n/a
30	TCF12	chr13:39611845-39612348	H1-hESC	embryonic stem cell:	n/a	chr13:39611852-39611859
31	MYC	chr13:39612080-39612659	HepG2	liver:	n/a	n/a
32	PML	chr13:39611758-39613178	GM12878	blood:	n/a	n/a
33	IRF1	chr13:39611937-39612843	K562	blood:	n/a	chr13:39612379-39612391
34	MYC	chr13:39611741-39612995	K562	blood:	n/a	n/a
35	POLR2A	chr13:39611684-39612342	GM12878	blood:	n/a	n/a
36	TBP	chr13:39611766-39612906	K562	blood:	n/a	n/a
37	MAX	chr13:39610127-39614057	NB4	blood:	n/a	chr13:39610504-39610514 chr13:39610831-39610839
38	POLR2A	chr13:39611493-39613152	GM12892	blood:	n/a	n/a
39	REST	chr13:39611994-39612315	PANC-1	pancreas:	n/a	chr13:39612005-39612025
40	RELA	chr13:39611918-39613052	GM15510	blood:	n/a	n/a
41	RCOR1	chr13:39611786-39613086	HepG2	liver:	n/a	n/a
42	POLR2A	chr13:39611551-39613699	GM18526	blood:	n/a	n/a
43	PML	chr13:39611619-39612366	MCF-7	breast:	n/a	n/a
44	SIN3AK20	chr13:39611824-39612863	HCT-116	colon:	n/a	n/a
45	USF1	chr13:39611971-39612688	SK-N-SH_RA	brain:	n/a	chr13:39612020-39612036
46	STAT1	chr13:39611945-39612982	GM12878	blood:	n/a	n/a
47	MXI1	chr13:39611827-39612902	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr13:39611754-39613056	GM10847	blood:	n/a	n/a
49	CREB1	chr13:39612056-39612302	A549	lung:	n/a	n/a
50	E2F6	chr13:39612259-39612986	Hela-S3	cervix:	n/a	chr13:39612491-39612502

No.	Distal block	Cell Line	Cell type
1	chr1:149223559..149225520-chr13:39611961..39613912,2	MCF-7	breast:
2	chr13:39259553..39261802-chr13:39611603..39613271,2	MCF-7	breast:
3	chr13:39584395..39587085-chr13:39611673..39614003,2	MCF-7	breast:
4	chr13:39610419..39613692-chr13:39616080..39618520,4	K562	blood:
5	chr13:39600178..39602849-chr13:39610760..39613364,3	K562	blood:
6	chr13:39611945..39612529-chr6:89791085..89792016,2	HCT-116	colon:
7	chr13:39611930..39612734-chr17:56406034..56406898,2	NB4	blood:
8	chr13:39596727..39599413-chr13:39610585..39613126,4	MCF-7	breast:

Variant related genes	Relation type
PROSER1	TF binding region
NHLRC3	TF binding region
ENSG00000146278	Chromatin interaction
ENSG00000005379	Chromatin interaction
ENSG00000150893	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000265148	Chromatin interaction
ENSG00000188811	Chromatin interaction
ENSG00000120685	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1012243	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1043348	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11147746	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12427448	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12428640	0.83[EUR][1000 genomes]
rs12428949	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12584883	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12585367	0.87[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17058909	0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs17059019	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17826235	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2148419	0.91[ASN][1000 genomes]
rs3751375	0.87[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60968029	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61737582	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6563659	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7323843	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73456199	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs943225	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2753642	chr13:39522300-39649000	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2753553	chr13:39526600-39649000	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 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	chr13:39609000-39615000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr13:39609000-39615200	Active TSS	K562	blood
3	chr13:39609200-39613600	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr13:39609200-39613800	Active TSS	GM12878-XiMat	blood
5	chr13:39609400-39613200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr13:39609400-39613400	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr13:39609400-39613400	Active TSS	NHLF	lung
8	chr13:39609400-39613800	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr13:39609400-39613800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr13:39609600-39612600	Active TSS	HMEC	breast
11	chr13:39609600-39613000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr13:39609600-39613200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr13:39609600-39613400	Active TSS	H9 Cell Line	embryonic stem cell
14	chr13:39609600-39613400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr13:39609600-39613400	Active TSS	Aorta	Aorta
16	chr13:39609600-39613400	Active TSS	Colon Smooth Muscle	Colon
17	chr13:39609600-39613400	Active TSS	Psoas Muscle	Psoas
18	chr13:39609600-39613400	Active TSS	Stomach Smooth Muscle	stomach
19	chr13:39609600-39613400	Active TSS	HSMMtube	muscle
20	chr13:39609600-39613600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr13:39609600-39613600	Active TSS	Ovary	ovary
22	chr13:39609600-39613600	Active TSS	Right Atrium	heart
23	chr13:39609600-39613600	Active TSS	Right Ventricle	heart
24	chr13:39609600-39613800	Active TSS	Fetal Muscle Leg	muscle
25	chr13:39609600-39613800	Active TSS	NHEK	skin
26	chr13:39609600-39614000	Active TSS	Hela-S3	cervix
27	chr13:39609600-39614200	Active TSS	Fetal Intestine Large	intestine
28	chr13:39609600-39614800	Active TSS	Placenta	Placenta
29	chr13:39609800-39613200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr13:39609800-39613400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr13:39609800-39613400	Active TSS	HSMM	muscle
32	chr13:39609800-39613600	Active TSS	H1 Cell Line	embryonic stem cell
33	chr13:39609800-39613600	Active TSS	Fetal Thymus	thymus
34	chr13:39609800-39613800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr13:39609800-39614400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr13:39610000-39612800	Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr13:39610000-39612800	Active TSS	NH-A	brain
38	chr13:39610000-39613000	Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr13:39610000-39613000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr13:39610000-39613200	Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr13:39610000-39613200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr13:39610000-39613200	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr13:39610000-39613200	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr13:39610000-39613400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr13:39610000-39613400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr13:39610000-39613400	Active TSS	NHDF-Ad	bronchial
47	chr13:39610000-39613600	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr13:39610000-39613600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr13:39610200-39613000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr13:39610200-39613200	Active TSS	Primary T helper naive cells from peripheral blood	blood

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