Variant report

Variant	rs11769941
Chromosome Location	chr7:38236504-38236505
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10046527	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10230858	0.82[GIH][hapmap]
rs10251985	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10259650	0.82[GIH][hapmap]
rs11769863	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12155411	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1990362	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1990363	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2037602	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2079849	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2534597	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2534598	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2534599	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4295563	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4339535	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4720271	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4723735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6969307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6973458	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6973870	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs756392	1.00[CEU][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7778240	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7778377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7787991	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7803902	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016355	chr7:38168232-38372719	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv830963	chr7:38172988-38344779	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2758112	chr7:38218703-38523455	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	esv2759524	chr7:38218703-38523455	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv427776	chr7:38218703-38523455	Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv830964	chr7:38218708-38390518	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv1030349	chr7:38227528-38372719	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv538818	chr7:38227528-38372719	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv1025974	chr7:38227528-38503472	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
10	nsv538819	chr7:38227528-38503472	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv433041	chr7:38229107-38358728	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11769941	VPS41	cis	cerebellum	SCAN
rs11769941	STARD3NL	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38218600-38259200	Weak transcription	Colonic Mucosa	Colon
2	chr7:38219600-38241400	Weak transcription	Fetal Intestine Large	intestine
3	chr7:38220200-38236800	Weak transcription	Fetal Stomach	stomach
4	chr7:38220200-38246600	Weak transcription	Fetal Thymus	thymus
5	chr7:38220200-38254800	Weak transcription	Brain Hippocampus Middle	brain
6	chr7:38220400-38247000	Weak transcription	Fetal Intestine Small	intestine
7	chr7:38221000-38246800	Weak transcription	Primary T cells from cord blood	blood
8	chr7:38223600-38255600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr7:38225000-38247000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr7:38227000-38237400	Weak transcription	Aorta	Aorta
11	chr7:38227600-38238400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr7:38228000-38236800	Weak transcription	Left Ventricle	heart
13	chr7:38228000-38256600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:38228200-38237400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr7:38228200-38237400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr7:38228200-38239400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:38228200-38241400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr7:38228200-38254400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr7:38228800-38239600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr7:38228800-38247200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr7:38229000-38236800	Weak transcription	Fetal Heart	heart
22	chr7:38229200-38249200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr7:38229600-38246600	Weak transcription	Primary B cells from cord blood	blood
24	chr7:38229800-38237400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr7:38229800-38246400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr7:38230200-38259200	Weak transcription	K562	blood
27	chr7:38230600-38241200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:38231400-38241800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:38231600-38247200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr7:38231800-38238800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr7:38232000-38246800	Weak transcription	Fetal Lung	lung
32	chr7:38232200-38237200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr7:38232400-38247200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr7:38232400-38255000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr7:38232600-38237200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr7:38232800-38255200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr7:38232800-38256000	Weak transcription	Fetal Brain Male	brain
38	chr7:38234400-38247200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr7:38235000-38239400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr7:38235200-38237600	Enhancers	Dnd41	blood
41	chr7:38235200-38238600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr7:38235200-38238600	Enhancers	HSMMtube	muscle
43	chr7:38235200-38251400	Weak transcription	Brain Angular Gyrus	brain
44	chr7:38235400-38237600	Enhancers	NHLF	lung
45	chr7:38235400-38238000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr7:38235400-38238400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr7:38235400-38238400	Enhancers	NHDF-Ad	bronchial
48	chr7:38235400-38238600	Enhancers	Muscle Satellite Cultured Cells	--
49	chr7:38235400-38238600	Enhancers	NH-A	brain
50	chr7:38235400-38239200	Enhancers	Osteobl	bone

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