Variant report

Variant	rs1190788
Chromosome Location	chr6:131520655-131520656
allele	C/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	RAD21	chr6:131520625-131521363	SK-N-SH	brain:	n/a	chr6:131520991-131521010 chr6:131521062-131521081 chr6:131520992-131521006
2	CTCF	chr6:131520580-131520730	GM12864	blood:	n/a	n/a
3	CTCF	chr6:131520646-131520732	GM10248	blood:	n/a	n/a
4	CTCF	chr6:131520580-131520730	HFF-Myc	foreskin:	n/a	n/a
5	CTCF	chr6:131520620-131520770	GM12865	blood:	n/a	n/a
6	CTCF	chr6:131520644-131520724	GM12878	blood:	n/a	n/a
7	SMC3	chr6:131520643-131521401	SK-N-SH	brain:	n/a	chr6:131521066-131521080
8	CTCF	chr6:131520620-131520770	HA-sp	spinal cord:	n/a	n/a

Variant related genes	Relation type
AKAP7	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10484763	0.81[YRI][hapmap];0.80[EUR][1000 genomes]
rs11154621	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap]
rs11154622	1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs11755717	1.00[CHB][hapmap]
rs11758994	1.00[CHB][hapmap]
rs11759793	0.81[EUR][1000 genomes]
rs1190794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190796	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190799	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190800	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190802	1.00[CEU][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1190805	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1190806	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1190809	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1190810	0.98[EUR][1000 genomes]
rs1190812	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11961577	0.81[EUR][1000 genomes]
rs1209159	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13195700	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap]
rs13200165	1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs13206776	1.00[CHB][hapmap]
rs1570348	1.00[CHB][hapmap]
rs1729549	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1729558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1746469	0.92[CEU][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs1746470	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1746471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1746473	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1746474	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17573187	1.00[CHB][hapmap]
rs17651753	1.00[CHB][hapmap]
rs17787964	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1885641	1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs2327102	0.80[EUR][1000 genomes]
rs28360555	0.82[EUR][1000 genomes]
rs34326915	0.81[EUR][1000 genomes]
rs34601891	0.80[EUR][1000 genomes]
rs35561719	0.80[EUR][1000 genomes]
rs3777474	0.95[EUR][1000 genomes]
rs3777476	1.00[CHB][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3777487	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs3850239	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3903759	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs4310080	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs4424112	1.00[CHB][hapmap]
rs56318353	1.00[ASN][1000 genomes]
rs66533103	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67021539	0.81[EUR][1000 genomes]
rs749375	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7743894	1.00[CHB][hapmap]
rs9492861	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs9492864	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9492865	1.00[CHB][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9492868	0.82[EUR][1000 genomes]
rs9492869	1.00[CHB][hapmap]
rs9492874	0.83[ASN][1000 genomes]
rs9492877	0.80[EUR][1000 genomes]
rs9492883	1.00[CHB][hapmap]

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
rs1190788	VNN1	cis	cerebellum	SCAN
rs1190788	AKAP7	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131457600-131520800	Weak transcription	Right Ventricle	heart
2	chr6:131488200-131534800	Weak transcription	Gastric	stomach
3	chr6:131505000-131521000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:131505000-131521800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:131505200-131522600	Weak transcription	HSMMtube	muscle
6	chr6:131505800-131534600	Weak transcription	Brain Substantia Nigra	brain
7	chr6:131505800-131534800	Weak transcription	Pancreas	Pancrea
8	chr6:131506400-131520800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr6:131506600-131520800	Weak transcription	Lung	lung
10	chr6:131506600-131523800	Weak transcription	HepG2	liver
11	chr6:131506600-131524000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:131506600-131529800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:131506600-131532000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:131506800-131551800	Weak transcription	Ovary	ovary
15	chr6:131510400-131534800	Weak transcription	Small Intestine	intestine
16	chr6:131513000-131520800	Weak transcription	Aorta	Aorta
17	chr6:131513000-131520800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr6:131513000-131522600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr6:131513000-131523000	Weak transcription	Placenta	Placenta
20	chr6:131513200-131526400	Weak transcription	Fetal Intestine Small	intestine
21	chr6:131513200-131536400	Weak transcription	Esophagus	oesophagus
22	chr6:131514400-131529800	Weak transcription	Brain Germinal Matrix	brain
23	chr6:131514400-131541400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:131514600-131521200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:131516600-131521200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:131517000-131520800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr6:131518200-131520800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr6:131518200-131520800	Enhancers	Primary T cells from cord blood	blood
29	chr6:131518200-131520800	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr6:131518200-131520800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:131518200-131521000	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr6:131518200-131521000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr6:131518200-131521200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr6:131518200-131525600	Weak transcription	Fetal Brain Male	brain
35	chr6:131518200-131531800	Weak transcription	Colon Smooth Muscle	Colon
36	chr6:131518400-131520800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr6:131518400-131521000	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr6:131518400-131521000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr6:131518400-131522600	Enhancers	Primary hematopoietic stem cells	blood
40	chr6:131518600-131520800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:131518600-131520800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:131518600-131520800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr6:131518600-131521000	Enhancers	Primary B cells from cord blood	blood
44	chr6:131518600-131521000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:131518800-131521000	Enhancers	Primary B cells from peripheral blood	blood
46	chr6:131518800-131521000	Enhancers	Primary T cells fromperipheralblood	blood
47	chr6:131518800-131521000	Enhancers	Fetal Thymus	thymus
48	chr6:131518800-131534600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr6:131519200-131521200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:131519200-131522600	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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