Variant report

Variant	rs6731096
Chromosome Location	chr2:11887435-11887436
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	POLR2A	chr2:11886456-11887536	K562	blood:	n/a	n/a
2	MAX	chr2:11884708-11887762	HepG2	liver:	n/a	chr2:11886898-11886908 chr2:11886778-11886787
3	POLR2A	chr2:11886620-11891581	GM12878	blood:	n/a	n/a
4	CTCF	chr2:11887360-11887510	NHEK	skin:	n/a	n/a
5	POLR2A	chr2:11886605-11887578	K562	blood:	n/a	n/a
6	CHD2	chr2:11886439-11887495	Hela-S3	cervix:	n/a	n/a
7	ELF1	chr2:11886103-11887523	GM12878	blood:	n/a	chr2:11886833-11886845 chr2:11886742-11886751
8	JUND	chr2:11887308-11887489	K562	blood:	n/a	n/a
9	MAX	chr2:11886355-11887595	K562	blood:	n/a	chr2:11886898-11886908 chr2:11886778-11886787
10	EP300	chr2:11886332-11887720	SK-N-SH	brain:	n/a	chr2:11887150-11887166 chr2:11886742-11886751
11	MXI1	chr2:11886239-11888165	IMR90	lung:	n/a	n/a
12	RUNX3	chr2:11887123-11887663	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:11886456-11887682	K562	blood:	n/a	n/a
14	MAX	chr2:11886448-11887591	SK-N-SH	brain:	n/a	chr2:11886898-11886908 chr2:11886778-11886787
15	CCNT2	chr2:11886434-11887437	K562	blood:	n/a	chr2:11886562-11886571
16	FOS	chr2:11887365-11887511	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr2:11886622-11887441	GM19193	blood:	n/a	n/a
18	MYC	chr2:11886483-11887517	A549	lung:	n/a	chr2:11886898-11886908 chr2:11886778-11886787
19	ESR1	chr2:11887096-11887467	ECC-1	luminal epithelium:	n/a	n/a
20	MAX	chr2:11886428-11887478	K562	blood:	n/a	chr2:11886898-11886908 chr2:11886778-11886787
21	MXI1	chr2:11886467-11887542	Hela-S3	cervix:	n/a	n/a
22	MYBL2	chr2:11887097-11887739	HepG2	liver:	n/a	n/a
23	POLR2A	chr2:11886473-11888191	GM18505	blood:	n/a	n/a
24	HDAC2	chr2:11886365-11887494	HepG2	liver:	n/a	chr2:11886423-11886431 chr2:11886529-11886543 chr2:11887222-11887236
25	MXI1	chr2:11886378-11887515	HepG2	liver:	n/a	n/a
26	TEAD4	chr2:11887132-11887509	H1-hESC	embryonic stem cell:	n/a	n/a
27	TCF7L2	chr2:11886479-11887482	HCT-116	colon:	n/a	n/a
28	SIN3A	chr2:11886214-11887595	H1-hESC	embryonic stem cell:	n/a	chr2:11887129-11887143
29	NR2F2	chr2:11886998-11887661	MCF-7	breast:	n/a	n/a
30	MXI1	chr2:11885917-11888799	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr2:11886595-11887823	Hela-S3	cervix:	n/a	n/a
32	E2F6	chr2:11886678-11887496	H1-hESC	embryonic stem cell:	n/a	chr2:11886745-11886754 chr2:11886982-11886994 chr2:11886743-11886753 chr2:11886982-11886991
33	TCF12	chr2:11886167-11887768	A549	lung:	n/a	chr2:11886616-11886626
34	POLR2A	chr2:11887254-11887534	HepG2	liver:	n/a	n/a
35	WRNIP1	chr2:11887183-11887667	GM12878	blood:	n/a	n/a
36	MAX	chr2:11886480-11887512	Hela-S3	cervix:	n/a	chr2:11886898-11886908 chr2:11886778-11886787
37	STAT5A	chr2:11887084-11887603	GM12878	blood:	n/a	n/a
38	RAD21	chr2:11887227-11887629	SK-N-SH_RA	brain:	n/a	n/a
39	CTCF	chr2:11887360-11887510	HEEpiC	esophagus:	n/a	n/a
40	RFX5	chr2:11886975-11887592	HepG2	liver:	n/a	chr2:11887309-11887324
41	CTCFL	chr2:11887307-11887445	K562	blood:	n/a	n/a
42	CTCF	chr2:11887300-11887450	SK-N-SH_RA	brain:	n/a	n/a
43	EP300	chr2:11887327-11887763	SK-N-SH_RA	brain:	n/a	n/a
44	MTA3	chr2:11886964-11887736	GM12878	blood:	n/a	n/a
45	MYC	chr2:11887296-11887473	MCF10A-Er-Src	breast:	n/a	n/a
46	CBX3	chr2:11886952-11887608	K562	blood:	n/a	n/a
47	MAZ	chr2:11886472-11887534	Hela-S3	cervix:	n/a	chr2:11886898-11886908 chr2:11886778-11886787
48	PBX3	chr2:11887254-11887824	SK-N-SH	brain:	n/a	n/a
49	GTF2F1	chr2:11887146-11887437	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr2:11886459-11887573	GM15510	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:11604255..11606398-chr2:11886112..11888104,2	K562	blood:
2	chr2:11886833..11889158-chr2:11909295..11910808,2	K562	blood:
3	chr2:11881178..11885762-chr2:11886043..11889477,7	MCF-7	breast:
4	chr2:10259345..10261058-chr2:11886635..11888299,2	K562	blood:
5	chr2:11885343..11888558-chr2:11916972..11921085,4	K562	blood:

Variant related genes	Relation type
ENSG00000230790	TF binding region
ENSG00000272524	Chromatin interaction
ENSG00000169016	Chromatin interaction
ENSG00000134324	Chromatin interaction
ENSG00000230790	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1006538	0.88[ASN][1000 genomes]
rs10169802	0.97[ASN][1000 genomes]
rs10185333	0.82[ASN][1000 genomes]
rs10191952	0.81[ASN][1000 genomes]
rs10191977	0.81[ASN][1000 genomes]
rs10192566	0.97[ASN][1000 genomes]
rs10205312	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10205400	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10207506	0.96[ASN][1000 genomes]
rs10208679	0.96[ASN][1000 genomes]
rs10209969	0.88[ASN][1000 genomes]
rs11676086	0.96[ASN][1000 genomes]
rs11676369	0.82[ASN][1000 genomes]
rs11693809	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11897144	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13407101	0.90[ASN][1000 genomes]
rs13409154	0.96[ASN][1000 genomes]
rs13412852	0.86[ASN][1000 genomes]
rs1469952	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2278513	0.82[ASN][1000 genomes]
rs2358041	0.86[ASN][1000 genomes]
rs2358042	0.86[ASN][1000 genomes]
rs4076055	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4129757	0.83[AMR][1000 genomes]
rs4315495	0.96[ASN][1000 genomes]
rs4669778	0.84[ASN][1000 genomes]
rs62113306	1.00[ASN][1000 genomes]
rs6717910	0.81[ASN][1000 genomes]
rs72773994	0.88[ASN][1000 genomes]
rs7595221	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs873358	0.96[ASN][1000 genomes]
rs893342	0.89[ASN][1000 genomes]
rs893345	0.82[ASN][1000 genomes]
rs893349	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
4	nsv580973	chr2:11864946-11898931	Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv580974	chr2:11867841-11898931	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 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	chr2:11886000-11888000	Active TSS	Brain Germinal Matrix	brain
2	chr2:11886200-11887800	Active TSS	HSMM	muscle
3	chr2:11886200-11888400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr2:11886200-11888600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr2:11886400-11887600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:11886400-11887600	Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr2:11886400-11887800	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr2:11886400-11888000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:11886400-11888000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:11886400-11888000	Active TSS	HSMMtube	muscle
11	chr2:11886600-11887600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:11886600-11887600	Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr2:11886600-11887600	Active TSS	Brain Angular Gyrus	brain
14	chr2:11886600-11887600	Active TSS	Brain Cingulate Gyrus	brain
15	chr2:11886600-11887600	Active TSS	Brain Substantia Nigra	brain
16	chr2:11886600-11887600	Active TSS	Fetal Stomach	stomach
17	chr2:11886600-11887600	Active TSS	Rectal Smooth Muscle	rectum
18	chr2:11886600-11887800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:11886600-11887800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:11886600-11887800	Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr2:11886600-11887800	Active TSS	Aorta	Aorta
22	chr2:11886600-11887800	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr2:11886600-11887800	Bivalent/Poised TSS	HepG2	liver
24	chr2:11886600-11887800	Active TSS	HMEC	breast
25	chr2:11886600-11887800	Active TSS	NHEK	skin
26	chr2:11886600-11888000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:11886600-11888000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:11886600-11888000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:11886600-11888000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:11886600-11888000	Active TSS	Esophagus	oesophagus
31	chr2:11886600-11888000	Active TSS	Left Ventricle	heart
32	chr2:11886600-11888000	Active TSS	Ovary	ovary
33	chr2:11886600-11888000	Active TSS	Right Atrium	heart
34	chr2:11886600-11888000	Active TSS	Right Ventricle	heart
35	chr2:11886600-11888000	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr2:11886600-11888000	Active TSS	GM12878-XiMat	blood
37	chr2:11886600-11888200	Active TSS	Psoas Muscle	Psoas
38	chr2:11886600-11888200	Active TSS	NHLF	lung
39	chr2:11886600-11888400	Active TSS	NHDF-Ad	bronchial
40	chr2:11886800-11887600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:11886800-11887600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:11886800-11887600	Active TSS	Lung	lung
43	chr2:11886800-11887800	Active TSS	Small Intestine	intestine
44	chr2:11886800-11888000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr2:11886800-11888000	Active TSS	Gastric	stomach
46	chr2:11886800-11888600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:11886800-11888800	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr2:11887000-11887600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
49	chr2:11887000-11887600	Flanking Active TSS	Placenta	Placenta
50	chr2:11887000-11887600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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