Variant report

Variant	rs3809122
Chromosome Location	chr12:56882710-56882711
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	E2F6	chr12:56882098-56882718	A549	lung:	n/a	chr12:56882362-56882373 chr12:56882401-56882413 chr12:56882365-56882372 chr12:56882361-56882373 chr12:56882365-56882372 chr12:56882365-56882372 chr12:56882679-56882691
2	E2F6	chr12:56881156-56882874	H1-hESC	embryonic stem cell:	n/a	chr12:56882362-56882373 chr12:56882401-56882413 chr12:56882762-56882771 chr12:56882365-56882372 chr12:56882361-56882373 chr12:56882365-56882372 chr12:56882365-56882372 chr12:56882679-56882691
3	MAX	chr12:56881023-56882909	ECC-1	luminal epithelium:	n/a	chr12:56881260-56881276 chr12:56881426-56881437 chr12:56882399-56882409 chr12:56882324-56882333
4	MAX	chr12:56881089-56882872	ECC-1	luminal epithelium:	n/a	chr12:56881260-56881276 chr12:56881426-56881437 chr12:56882399-56882409 chr12:56882324-56882333
5	POLR2A	chr12:56882643-56882840	ProgFib	skin:	n/a	n/a
6	MAX	chr12:56881156-56882802	H1-hESC	embryonic stem cell:	n/a	chr12:56881260-56881276 chr12:56881426-56881437 chr12:56882399-56882409 chr12:56882324-56882333
7	MAX	chr12:56882013-56882740	A549	lung:	n/a	chr12:56882399-56882409 chr12:56882324-56882333
8	TCF12	chr12:56881138-56882726	ECC-1	luminal epithelium:	n/a	n/a
9	MAX	chr12:56881150-56882787	HepG2	liver:	n/a	chr12:56881260-56881276 chr12:56881426-56881437 chr12:56882399-56882409 chr12:56882324-56882333
10	ZNF263	chr12:56880760-56883087	HEK293-T-REx	kidney:	n/a	n/a
11	MAX	chr12:56881191-56882820	MCF-7	breast:	n/a	chr12:56881260-56881276 chr12:56881426-56881437 chr12:56882399-56882409 chr12:56882324-56882333
12	MAX	chr12:56881149-56882807	HepG2	liver:	n/a	chr12:56881260-56881276 chr12:56881426-56881437 chr12:56882399-56882409 chr12:56882324-56882333
13	ELF1	chr12:56881185-56882797	GM12878	blood:	n/a	n/a
14	MAX	chr12:56881084-56882832	H1-hESC	embryonic stem cell:	n/a	chr12:56881260-56881276 chr12:56881426-56881437 chr12:56882399-56882409 chr12:56882324-56882333
15	MAX	chr12:56881952-56882834	A549	lung:	n/a	chr12:56882399-56882409 chr12:56882324-56882333
16	E2F6	chr12:56880936-56883052	H1-hESC	embryonic stem cell:	n/a	chr12:56882362-56882373 chr12:56882401-56882413 chr12:56882762-56882771 chr12:56882365-56882372 chr12:56882361-56882373 chr12:56882365-56882372 chr12:56882365-56882372 chr12:56882679-56882691
17	E2F6	chr12:56881977-56882862	A549	lung:	n/a	chr12:56882362-56882373 chr12:56882401-56882413 chr12:56882762-56882771 chr12:56882365-56882372 chr12:56882361-56882373 chr12:56882365-56882372 chr12:56882365-56882372 chr12:56882679-56882691

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:56882693-56882743	AG09319	gingival:	n/a
2	chr12:56882693-56882743	GM19239	blood:	n/a
3	chr12:56882693-56882743	IMR90	lung:	fetal
4	chr12:56882693-56882743	BE2_C	brain:	n/a
5	chr12:56882693-56882743	NHBE	bronchial:	n/a
6	chr12:56882693-56882743	HCPEpiC	choroid plexus:	n/a
7	chr12:56882693-56882743	NH-A	brain:	n/a
8	chr12:56882693-56882743	AG09309	skin:	n/a
9	chr12:56882693-56882743	PFSK-1	brain:	n/a
10	chr12:56882693-56882743	SKMC	muscle:	n/a
11	chr12:56882693-56882743	ProgFib	skin:	n/a
12	chr12:56882693-56882743	AG04449	skin:	fetal
13	chr12:56882693-56882743	HNPCEpiC	eye:	n/a
14	chr12:56882693-56882743	SK-N-MC	brain:	n/a
15	chr12:56882693-56882743	RPTEC	kidney:	n/a
16	chr12:56882693-56882743	SK-N-SH	brain:	n/a
17	chr12:56882693-56882743	Jurkat	blood:	n/a
18	chr12:56882693-56882743	GM12891	blood:	n/a
19	chr12:56882693-56882743	MCF-7	breast:	n/a
20	chr12:56882693-56882743	U87	brain:	n/a
21	chr12:56882693-56882743	NT2-D1	testis:	n/a
22	chr12:56882693-56882743	HCM	heart:	n/a
23	chr12:56882693-56882743	PrEC	prostate:	n/a
24	chr12:56882693-56882743	GM12892	blood:	n/a
25	chr12:56882693-56882743	HMEC	breast:	n/a
26	chr12:56882693-56882743	A549	lung:	n/a
27	chr12:56882693-56882743	AoSMC	blood vessel:	n/a
28	chr12:56882693-56882743	ECC-1	luminal epithelium:	n/a
29	chr12:56882693-56882743	HCT-116	colon:	n/a
30	chr12:56882693-56882743	ovcar-3	ovarian:	n/a
31	chr12:56882693-56882743	HIPEpiC	eye:	n/a
32	chr12:56882693-56882743	HCF	heart:	n/a
33	chr12:56882693-56882743	HAEpiC	amniotic membrane:	n/a
34	chr12:56882693-56882743	CMK	blood:	n/a
35	chr12:56882693-56882743	HEK293	kidney:	embryo
36	chr12:56882693-56882743	NB4	blood:	n/a
37	chr12:56882693-56882743	HRCEpiC	kidney:	n/a
38	chr12:56882693-56882743	HUVEC	blood vessel:	n/a
39	chr12:56882693-56882743	GM06990	blood:	n/a
40	chr12:56882693-56882743	SK-N-SH_RA	brain:	n/a
41	chr12:56882693-56882743	T-47D	breast:	n/a
42	chr12:56882693-56882743	AG10803	skin:	n/a
43	chr12:56882693-56882743	Caco-2	colon:	n/a
44	chr12:56882693-56882743	MCF10A-Er-Src	breast:	n/a
45	chr12:56882693-56882743	HPAEpiC	pulmonary alveolar:	n/a
46	chr12:56882693-56882743	HRPEpiC	eye:	n/a
47	chr12:56882693-56882743	GM12878	blood:	n/a
48	chr12:56882693-56882743	AG04450	lung:	fetal
49	chr12:56882693-56882743	HL-60	blood:	n/a
50	chr12:56882693-56882743	SAEC	small airway:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56614067..56616141-chr12:56881501..56883346,2	MCF-7	breast:
2	chr12:56841673..56844476-chr12:56882161..56884243,2	MCF-7	breast:

Variant related genes	Relation type
GLS2	TF binding region
GLS2	CpG island
ENSG00000181852	Chromatin interaction
ENSG00000111602	Chromatin interaction
ENSG00000139579	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10876895	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11171862	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171863	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171865	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171870	0.82[ASN][1000 genomes]
rs12304519	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12316930	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12809550	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12813881	0.84[ASN][1000 genomes]
rs2638285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2638318	0.84[EUR][1000 genomes]
rs2638319	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs2638330	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2638334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2657877	0.83[YRI][hapmap]
rs2657909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34287864	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs58252713	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6581096	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71459375	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71459376	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7314242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv1052713	chr12:56848036-56917602	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	35 gene(s)	inside rSNPs	diseases
4	esv3326032	chr12:56881235-56884033	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3809122	RBMS2	Cis_1M	lymphoblastoid	RTeQTL
rs3809122	SPRYD4	Cis_1M	lymphoblastoid	RTeQTL
rs3809122	FUT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56880800-56882800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
2	chr12:56880800-56882800	Active TSS	Brain Angular Gyrus	brain
3	chr12:56880800-56882800	Active TSS	Brain Substantia Nigra	brain
4	chr12:56881000-56882800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr12:56881200-56882800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
6	chr12:56881200-56882800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr12:56881200-56882800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:56881200-56882800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:56881200-56882800	Flanking Active TSS	Right Ventricle	heart
10	chr12:56881200-56882800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
11	chr12:56881400-56882800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
12	chr12:56881400-56882800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
13	chr12:56881400-56882800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
14	chr12:56881400-56882800	Active TSS	Brain Anterior Caudate	brain
15	chr12:56881400-56882800	Active TSS	Colon Smooth Muscle	Colon
16	chr12:56881800-56882800	Active TSS	Sigmoid Colon	Sigmoid Colon
17	chr12:56882000-56882800	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
18	chr12:56882000-56882800	Active TSS	Brain Cingulate Gyrus	brain
19	chr12:56882200-56882800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr12:56882200-56882800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
21	chr12:56882200-56882800	Bivalent Enhancer	Fetal Brain Male	brain
22	chr12:56882200-56882800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
23	chr12:56882200-56882800	Enhancers	Spleen	Spleen
24	chr12:56882400-56882800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:56882400-56882800	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:56882400-56882800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr12:56882400-56882800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr12:56882400-56882800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:56882400-56882800	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr12:56882400-56882800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
31	chr12:56882400-56882800	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr12:56882400-56882800	Enhancers	Fetal Heart	heart
33	chr12:56882400-56882800	Bivalent Enhancer	Placenta	Placenta
34	chr12:56882400-56882800	Bivalent Enhancer	Fetal Thymus	thymus
35	chr12:56882400-56882800	Bivalent Enhancer	Stomach Mucosa	stomach
36	chr12:56882400-56882800	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr12:56882400-56882800	Bivalent/Poised TSS	HSMM	muscle
38	chr12:56882400-56882800	Bivalent Enhancer	HUVEC	blood vessel
39	chr12:56882600-56882800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:56882600-56882800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr12:56882600-56882800	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr12:56882600-56882800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
43	chr12:56882600-56882800	Bivalent Enhancer	Primary B cells from cord blood	blood
44	chr12:56882600-56882800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
45	chr12:56882600-56882800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr12:56882600-56882800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:56882600-56882800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
48	chr12:56882600-56882800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:56882600-56882800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:56882600-56882800	Enhancers	Primary T killer memory cells from peripheral blood	blood

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