Variant report

Variant	rs56138205
Chromosome Location	chr10:52384362-52384363
allele	C/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	POLR2A	chr10:52383364-52385552	GM12878	blood:	n/a	n/a
2	ELF1	chr10:52382439-52385283	GM12878	blood:	n/a	chr10:52385128-52385140 chr10:52384980-52384989
3	MAX	chr10:52383421-52385509	ECC-1	luminal epithelium:	n/a	chr10:52384447-52384456 chr10:52384446-52384456 chr10:52384445-52384454
4	YY1	chr10:52384162-52385584	SK-N-SH_RA	brain:	n/a	chr10:52385126-52385135 chr10:52384570-52384584 chr10:52385126-52385137
5	FOXM1	chr10:52384170-52384643	GM12878	blood:	n/a	n/a
6	MAX	chr10:52383402-52385378	SK-N-SH	brain:	n/a	chr10:52384447-52384456 chr10:52384446-52384456 chr10:52384445-52384454
7	SP1	chr10:52383337-52385386	HCT-116	colon:	n/a	chr10:52384344-52384356 chr10:52384344-52384356 chr10:52384345-52384354 chr10:52385059-52385072 chr10:52384346-52384355 chr10:52383448-52383457 chr10:52384345-52384354
8	TAF1	chr10:52384075-52384637	PFSK-1	brain:	n/a	n/a
9	ELF1	chr10:52384109-52385190	HepG2	liver:	n/a	chr10:52385128-52385140 chr10:52384980-52384989
10	MAFK	chr10:52383950-52385790	K562	blood:	n/a	n/a
11	PBX3	chr10:52384115-52385332	SK-N-SH	brain:	n/a	n/a
12	MYC	chr10:52383967-52384522	MCF10A-Er-Src	breast:	n/a	chr10:52384447-52384456 chr10:52384446-52384456 chr10:52384445-52384454
13	TEAD4	chr10:52383429-52385947	K562	blood:	n/a	n/a
14	NRF1	chr10:52384246-52384596	K562	blood:	n/a	chr10:52384430-52384441 chr10:52384430-52384444 chr10:52384427-52384441 chr10:52384430-52384441
15	POLR2A	chr10:52384184-52385177	A549	lung:	n/a	n/a
16	POLR2A	chr10:52383376-52385992	U87	brain:	n/a	n/a
17	TAF1	chr10:52384181-52385183	HepG2	liver:	n/a	n/a
18	MAX	chr10:52383304-52385178	HUVEC	blood vessel:	n/a	chr10:52384447-52384456 chr10:52384446-52384456 chr10:52384445-52384454
19	USF1	chr10:52384207-52385539	SK-N-SH	brain:	n/a	chr10:52384828-52384844 chr10:52384677-52384688 chr10:52385126-52385142
20	POLR2A	chr10:52381694-52385975	Hela-S3	cervix:	n/a	n/a
21	BRCA1	chr10:52384328-52384457	H1-hESC	embryonic stem cell:	n/a	n/a
22	EGR1	chr10:52384293-52384505	GM12878	blood:	n/a	n/a
23	RCOR1	chr10:52383404-52385746	K562	blood:	n/a	n/a
24	MXI1	chr10:52381308-52386209	SK-N-SH	brain:	n/a	chr10:52384448-52384457 chr10:52384446-52384455
25	GABPA	chr10:52384151-52385306	HL-60	blood:	n/a	chr10:52384430-52384441 chr10:52384430-52384444 chr10:52384427-52384441
26	POLR2A	chr10:52383148-52385231	A549	lung:	n/a	n/a
27	THAP1	chr10:52384202-52384971	K562	blood:	n/a	n/a
28	FOS	chr10:52384217-52384506	MCF10A-Er-Src	breast:	n/a	chr10:52384395-52384409 chr10:52384342-52384351 chr10:52384347-52384356
29	YY1	chr10:52384264-52385186	HepG2	liver:	n/a	chr10:52385126-52385135 chr10:52384570-52384584 chr10:52385126-52385137
30	CBX3	chr10:52383949-52384597	K562	blood:	n/a	n/a
31	POLR2A	chr10:52383216-52385848	GM12892	blood:	n/a	n/a
32	MAX	chr10:52382912-52385590	A549	lung:	n/a	chr10:52384447-52384456 chr10:52384446-52384456 chr10:52384445-52384454
33	E2F6	chr10:52383388-52385165	H1-hESC	embryonic stem cell:	n/a	chr10:52383483-52383493 chr10:52384118-52384132 chr10:52383640-52383649 chr10:52384541-52384553
34	MAZ	chr10:52382568-52385628	Hela-S3	cervix:	n/a	chr10:52384447-52384456 chr10:52384446-52384456 chr10:52384445-52384454
35	RXRA	chr10:52384213-52384512	GM12878	blood:	n/a	n/a
36	IRF1	chr10:52383560-52385932	K562	blood:	n/a	chr10:52383896-52383910 chr10:52384342-52384356 chr10:52385614-52385630 chr10:52384250-52384264
37	ZNF143	chr10:52384097-52385218	Hela-S3	cervix:	n/a	n/a
38	EBF1	chr10:52383564-52385457	GM12878	blood:	n/a	chr10:52385203-52385212 chr10:52384007-52384020 chr10:52384009-52384018 chr10:52385202-52385212 chr10:52385201-52385214 chr10:52384008-52384019
39	CTCF	chr10:52384260-52384410	HBMEC	blood vessel:	n/a	n/a
40	TAF1	chr10:52384049-52385408	K562	blood:	n/a	n/a
41	RELA	chr10:52382955-52385813	GM15510	blood:	n/a	n/a
42	YY1	chr10:52383861-52385476	H1-hESC	embryonic stem cell:	n/a	chr10:52385126-52385135 chr10:52384570-52384584 chr10:52385126-52385137 chr10:52384015-52384026
43	POLR2A	chr10:52384181-52385165	HepG2	liver:	n/a	n/a
44	ATF1	chr10:52384112-52385291	K562	blood:	n/a	n/a
45	MYC	chr10:52384216-52385180	HepG2	liver:	n/a	chr10:52384447-52384456 chr10:52384446-52384456 chr10:52384445-52384454
46	POLR2A	chr10:52384085-52385141	SK-N-SH	brain:	n/a	n/a
47	RAD21	chr10:52383910-52384466	SK-N-SH_RA	brain:	n/a	n/a
48	TRIM28	chr10:52384001-52385815	K562	blood:	n/a	chr10:52385807-52385815 chr10:52385790-52385798
49	MXI1	chr10:52383092-52385294	HepG2	liver:	n/a	chr10:52384448-52384457 chr10:52384446-52384455
50	EP300	chr10:52383747-52385832	K562	blood:	n/a	chr10:52384373-52384389 chr10:52385763-52385776 chr10:52384377-52384393 chr10:52384821-52384837

No.	Distal block	Cell Line	Cell type
1	chr10:52173595..52180106-chr10:52381535..52385847,7	MCF-7	breast:
2	chr10:52383783..52384592-chr11:82866965..82867887,2	Hela-S3	cervix:
3	chr10:52384254..52384940-chr8:11659944..11660800,2	NB4	blood:
4	chr10:52342227..52348125-chr10:52381237..52386507,8	K562	blood:
5	chr10:52229715..52232627-chr10:52381775..52384727,3	MCF-7	breast:
6	chr10:52341787..52346100-chr10:52382899..52385718,8	MCF-7	breast:
7	chr10:52176732..52178529-chr10:52382760..52384432,2	MCF-7	breast:
8	chr10:52381243..52386496-chr10:52418227..52421959,6	MCF-7	breast:
9	chr10:52382538..52386733-chr10:52497918..52501112,4	MCF-7	breast:
10	chr10:52358660..52367648-chr10:52378481..52386533,25	MCF-7	breast:
11	chr10:52383877..52384519-chr12:12509876..12510586,2	Hela-S3	cervix:
12	chr10:52103151..52105270-chr10:52383748..52386662,2	K562	blood:
13	chr10:52383702..52384672-chr20:62496300..62497011,2	Hela-S3	cervix:
14	chr10:52365691..52371767-chr10:52381261..52385919,7	K562	blood:
15	chr10:52173619..52179913-chr10:52381938..52386991,6	K562	blood:
16	chr10:52343887..52348125-chr10:52383719..52386062,5	K562	blood:
17	chr10:52229968..52233210-chr10:52382214..52385931,3	MCF-7	breast:
18	chr10:52356810..52366659-chr10:52378806..52385975,25	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ASAH2B-2	chr10:52383739-52386623	NONHSAT013388

Variant related genes	Relation type
ENSG00000226200	TF binding region
SGMS1	TF binding region
ENSG00000204147	Chromatin interaction
ENSG00000165714	Chromatin interaction
ENSG00000079459	Chromatin interaction
ENSG00000101150	Chromatin interaction
ENSG00000198964	Chromatin interaction
ENSG00000251950	Chromatin interaction
ENSG00000255046	Chromatin interaction
ENSG00000225303	Chromatin interaction
ENSG00000231345	Chromatin interaction
ENSG00000205791	Chromatin interaction
ENSG00000230036	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10826243	0.89[EUR][1000 genomes]
rs12358192	0.90[EUR][1000 genomes]
rs12358866	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3001854	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7093195	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7919879	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52380800-52385400	Active TSS	Rectal Smooth Muscle	rectum
2	chr10:52381200-52386000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr10:52381400-52384400	Active TSS	Right Atrium	heart
4	chr10:52381400-52385400	Active TSS	Brain Cingulate Gyrus	brain
5	chr10:52381400-52385800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr10:52381400-52386000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr10:52381400-52386200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr10:52381600-52385200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
9	chr10:52381600-52385200	Active TSS	Primary T killer memory cells from peripheral blood	blood
10	chr10:52381600-52385200	Active TSS	Brain Hippocampus Middle	brain
11	chr10:52381600-52385400	Active TSS	Psoas Muscle	Psoas
12	chr10:52381600-52385600	Active TSS	Colon Smooth Muscle	Colon
13	chr10:52381600-52385600	Active TSS	Left Ventricle	heart
14	chr10:52381600-52385600	Active TSS	Ovary	ovary
15	chr10:52381600-52385800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr10:52381600-52385800	Active TSS	H9 Cell Line	embryonic stem cell
17	chr10:52381600-52385800	Active TSS	Fetal Heart	heart
18	chr10:52381800-52385200	Active TSS	Primary T cells from cord blood	blood
19	chr10:52381800-52385400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr10:52381800-52385400	Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr10:52381800-52385400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr10:52381800-52385400	Active TSS	Brain Angular Gyrus	brain
23	chr10:52381800-52385400	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr10:52381800-52385400	Active TSS	Brain Substantia Nigra	brain
25	chr10:52381800-52385400	Active TSS	Fetal Intestine Small	intestine
26	chr10:52381800-52385400	Active TSS	Fetal Kidney	kidney
27	chr10:52381800-52385400	Active TSS	Lung	lung
28	chr10:52381800-52385400	Active TSS	Small Intestine	intestine
29	chr10:52381800-52385400	Active TSS	Spleen	Spleen
30	chr10:52381800-52385400	Active TSS	GM12878-XiMat	blood
31	chr10:52381800-52385400	Active TSS	HSMMtube	muscle
32	chr10:52381800-52385600	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr10:52381800-52385600	Active TSS	Gastric	stomach
34	chr10:52381800-52385600	Active TSS	Pancreas	Pancrea
35	chr10:52381800-52385600	Active TSS	Right Ventricle	heart
36	chr10:52381800-52385600	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr10:52381800-52385800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr10:52381800-52385800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr10:52381800-52385800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr10:52381800-52385800	Active TSS	A549	lung
41	chr10:52381800-52386000	Active TSS	Fetal Intestine Large	intestine
42	chr10:52382000-52385200	Active TSS	Liver	Liver
43	chr10:52382000-52385200	Active TSS	Brain Anterior Caudate	brain
44	chr10:52382000-52385200	Active TSS	Thymus	Thymus
45	chr10:52382000-52385600	Active TSS	Aorta	Aorta
46	chr10:52382000-52385800	Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr10:52382200-52385200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr10:52382200-52385200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr10:52382200-52385200	Active TSS	Fetal Stomach	stomach
50	chr10:52382200-52385400	Active TSS	Fetal Lung	lung

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