Variant report

Variant	rs3903759
Chromosome Location	chr6:131520994-131520995
allele	A/C
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	CTCF	chr6:131520871-131521109	MCF-7	breast:	n/a	chr6:131520992-131521013 chr6:131521064-131521082
2	CTCF	chr6:131520940-131521090	BJ	skin:	n/a	chr6:131520992-131521013 chr6:131521064-131521082
3	CTCF	chr6:131520940-131521090	AG04449	skin:	n/a	chr6:131520992-131521013 chr6:131521064-131521082
4	CTCF	chr6:131520773-131521278	GM12878	blood:	n/a	chr6:131520992-131521013 chr6:131521064-131521082
5	CTCF	chr6:131520920-131521070	Hela-S3	cervix:	n/a	chr6:131520992-131521013
6	MYC	chr6:131520902-131521026	MCF10A-Er-Src	breast:	n/a	n/a
7	CTCF	chr6:131520960-131521110	GM12869	blood:	n/a	chr6:131520992-131521013 chr6:131521064-131521082
8	CTCF	chr6:131520880-131521030	HFF-Myc	foreskin:	n/a	chr6:131520992-131521013
9	CTCF	chr6:131520860-131521134	MCF-7	breast:	n/a	chr6:131520992-131521013 chr6:131521064-131521082
10	POU2F2	chr6:131520785-131521264	GM12891	blood:	n/a	chr6:131521041-131521051 chr6:131521040-131521054 chr6:131521043-131521050
11	E2F4	chr6:131520917-131521117	MCF10A-Er-Src	breast:	n/a	n/a
12	RAD21	chr6:131520787-131521263	A549	lung:	n/a	chr6:131520991-131521010 chr6:131521062-131521081 chr6:131520992-131521006
13	TBL1XR1	chr6:131520903-131521159	GM12878	blood:	n/a	n/a
14	RAD21	chr6:131520674-131521412	MCF-7	breast:	n/a	chr6:131520991-131521010 chr6:131521062-131521081 chr6:131520992-131521006
15	CTCF	chr6:131520920-131521070	BJ	skin:	n/a	chr6:131520992-131521013
16	CTCF	chr6:131520824-131521164	IMR90	lung:	n/a	chr6:131520992-131521013 chr6:131521064-131521082
17	CTCF	chr6:131520818-131521134	GM12891	blood:	n/a	chr6:131520992-131521013 chr6:131521064-131521082
18	CTCF	chr6:131520960-131521110	GM12878	blood:	n/a	chr6:131520992-131521013 chr6:131521064-131521082
19	CTCF	chr6:131520960-131521110	HPF	lung:	n/a	chr6:131520992-131521013 chr6:131521064-131521082
20	RELA	chr6:131520827-131521268	GM19099	blood:	n/a	n/a
21	CTCF	chr6:131520835-131521083	ECC-1	luminal epithelium:	n/a	chr6:131520992-131521013 chr6:131521064-131521082
22	RAD21	chr6:131520716-131521212	HepG2	liver:	n/a	chr6:131520991-131521010 chr6:131521062-131521081 chr6:131520992-131521006
23	FOXA1	chr6:131520852-131521111	T-47D	breast:	n/a	n/a
24	POU2F2	chr6:131520812-131521183	GM12878	blood:	n/a	chr6:131521041-131521051 chr6:131521040-131521054 chr6:131521043-131521050
25	CTCF	chr6:131520920-131521070	HEK293	kidney:	n/a	chr6:131520992-131521013
26	CTCF	chr6:131520882-131521104	SK-N-SH_RA	brain:	n/a	chr6:131520992-131521013 chr6:131521064-131521082
27	CTCF	chr6:131520880-131521030	Hela-S3	cervix:	n/a	chr6:131520992-131521013
28	FOXP2	chr6:131520819-131521270	SK-N-MC	brain:	n/a	n/a
29	RUNX3	chr6:131520724-131521313	GM12878	blood:	n/a	n/a
30	CTCF	chr6:131520940-131521090	GM12870	blood:	n/a	chr6:131520992-131521013 chr6:131521064-131521082
31	MTA3	chr6:131520732-131521411	GM12878	blood:	n/a	n/a
32	POU2F2	chr6:131520741-131521272	GM12878	blood:	n/a	chr6:131521041-131521051 chr6:131521040-131521054 chr6:131521043-131521050
33	CTCF	chr6:131520843-131521125	MCF-7	breast:	n/a	chr6:131520992-131521013 chr6:131521064-131521082
34	CTCF	chr6:131520699-131521363	A549	lung:	n/a	chr6:131520992-131521013 chr6:131521064-131521082
35	CTCF	chr6:131520960-131521110	WI-38	lung:	n/a	chr6:131520992-131521013 chr6:131521064-131521082
36	CTCF	chr6:131520920-131521070	HMEC	breast:	n/a	chr6:131520992-131521013
37	JUND	chr6:131520892-131521130	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr6:131520789-131521242	H1-hESC	embryonic stem cell:	n/a	chr6:131520992-131521013 chr6:131521064-131521082
39	MXI1	chr6:131520795-131521108	GM12878	blood:	n/a	n/a
40	STAT1	chr6:131520766-131521122	GM12878	blood:	n/a	n/a
41	CTCF	chr6:131520960-131521110	GM12864	blood:	n/a	chr6:131520992-131521013 chr6:131521064-131521082
42	CEBPB	chr6:131520797-131521134	HepG2	liver:	n/a	n/a
43	CTCF	chr6:131520920-131521070	HMF	breast:	n/a	chr6:131520992-131521013
44	NFYB	chr6:131520955-131521199	GM12878	blood:	n/a	n/a
45	CTCF	chr6:131520717-131521234	MCF-7	breast:	n/a	chr6:131520992-131521013 chr6:131521064-131521082
46	GTF2F1	chr6:131520940-131521124	H1-hESC	embryonic stem cell:	n/a	n/a
47	RAD21	chr6:131520854-131521244	GM12878	blood:	n/a	chr6:131520991-131521010 chr6:131521062-131521081 chr6:131520992-131521006
48	CTCF	chr6:131520920-131521070	AG09319	gingival:	n/a	chr6:131520992-131521013
49	RAD21	chr6:131520625-131521363	SK-N-SH	brain:	n/a	chr6:131520991-131521010 chr6:131521062-131521081 chr6:131520992-131521006
50	CTCF	chr6:131520920-131521070	AoAF	blood vessel:	n/a	chr6:131520992-131521013

Variant related genes	Relation type
AKAP7	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11154621	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs11154622	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs11754401	0.84[ASN][1000 genomes]
rs11755717	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs11758994	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs11759793	0.84[ASN][1000 genomes]
rs11759926	0.84[ASN][1000 genomes]
rs1190788	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs1190794	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1190796	0.91[ASN][1000 genomes]
rs1190799	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs1190800	0.91[ASN][1000 genomes]
rs1190801	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1190805	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1190806	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11961577	0.84[ASN][1000 genomes]
rs1209159	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1317667	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13195700	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs13200165	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs13205441	0.84[ASN][1000 genomes]
rs13206776	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs1570348	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1729549	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs1729558	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1746470	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs1746471	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs1746473	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs1746474	0.91[ASN][1000 genomes]
rs17573187	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17651753	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17787964	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1885641	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2077490	0.84[ASN][1000 genomes]
rs2327102	0.84[ASN][1000 genomes]
rs28360555	0.84[ASN][1000 genomes]
rs34326915	0.84[ASN][1000 genomes]
rs34601891	0.84[ASN][1000 genomes]
rs35017713	0.84[ASN][1000 genomes]
rs35561719	0.84[ASN][1000 genomes]
rs35746376	0.84[ASN][1000 genomes]
rs3777476	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs3777487	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777489	0.84[ASN][1000 genomes]
rs3777493	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3850239	0.84[ASN][1000 genomes]
rs4310080	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs4424112	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs56189731	0.83[EUR][1000 genomes]
rs56318353	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66533103	0.84[ASN][1000 genomes]
rs67021539	0.84[ASN][1000 genomes]
rs67399092	0.84[ASN][1000 genomes]
rs6937607	0.83[EUR][1000 genomes]
rs73631985	0.81[EUR][1000 genomes]
rs73634710	0.83[EUR][1000 genomes]
rs749375	0.84[ASN][1000 genomes]
rs7743894	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7754007	0.83[EUR][1000 genomes]
rs9483238	0.84[ASN][1000 genomes]
rs9492861	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492864	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs9492865	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs9492868	0.84[ASN][1000 genomes]
rs9492869	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs9492874	0.92[ASN][1000 genomes]
rs9492877	0.84[ASN][1000 genomes]
rs9492880	0.84[ASN][1000 genomes]
rs9492883	1.00[CHB][hapmap];0.84[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	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv830807	chr6:131390952-131581931	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv886664	chr6:131443843-131754930	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv886665	chr6:131518894-131611309	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3903759	VNN1	cis	cerebellum	SCAN
rs3903759	VNN3	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131488200-131534800	Weak transcription	Gastric	stomach
2	chr6:131505000-131521000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:131505000-131521800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:131505200-131522600	Weak transcription	HSMMtube	muscle
5	chr6:131505800-131534600	Weak transcription	Brain Substantia Nigra	brain
6	chr6:131505800-131534800	Weak transcription	Pancreas	Pancrea
7	chr6:131506600-131523800	Weak transcription	HepG2	liver
8	chr6:131506600-131524000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:131506600-131529800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:131506600-131532000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:131506800-131551800	Weak transcription	Ovary	ovary
12	chr6:131510400-131534800	Weak transcription	Small Intestine	intestine
13	chr6:131513000-131522600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr6:131513000-131523000	Weak transcription	Placenta	Placenta
15	chr6:131513200-131526400	Weak transcription	Fetal Intestine Small	intestine
16	chr6:131513200-131536400	Weak transcription	Esophagus	oesophagus
17	chr6:131514400-131529800	Weak transcription	Brain Germinal Matrix	brain
18	chr6:131514400-131541400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:131514600-131521200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr6:131516600-131521200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:131518200-131521000	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr6:131518200-131521000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:131518200-131521200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr6:131518200-131525600	Weak transcription	Fetal Brain Male	brain
25	chr6:131518200-131531800	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:131518400-131521000	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr6:131518400-131521000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr6:131518400-131522600	Enhancers	Primary hematopoietic stem cells	blood
29	chr6:131518600-131521000	Enhancers	Primary B cells from cord blood	blood
30	chr6:131518600-131521000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:131518800-131521000	Enhancers	Primary B cells from peripheral blood	blood
32	chr6:131518800-131521000	Enhancers	Primary T cells fromperipheralblood	blood
33	chr6:131518800-131521000	Enhancers	Fetal Thymus	thymus
34	chr6:131518800-131534600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr6:131519200-131521200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:131519200-131522600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr6:131519400-131521000	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr6:131519400-131521000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr6:131519600-131521200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:131519800-131521200	Strong transcription	Stomach Smooth Muscle	stomach
41	chr6:131520000-131522400	Strong transcription	Brain Anterior Caudate	brain
42	chr6:131520200-131521200	Enhancers	Dnd41	blood
43	chr6:131520200-131521600	Strong transcription	Adipose Nuclei	Adipose
44	chr6:131520400-131521800	Strong transcription	Liver	Liver
45	chr6:131520600-131521000	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr6:131520600-131521000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr6:131520600-131521000	Strong transcription	Psoas Muscle	Psoas
48	chr6:131520600-131521000	Genic enhancers	Thymus	Thymus
49	chr6:131520600-131521200	Strong transcription	Fetal Lung	lung
50	chr6:131520600-131521200	Enhancers	GM12878-XiMat	blood

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