Variant report

Variant	rs1990362
Chromosome Location	chr7:38234690-38234691
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:38233687..38235953-chr7:38237022..38238979,2	K562	blood:
2	chr7:38227891..38230649-chr7:38232228..38236462,5	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10046527	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10230858	0.82[GIH][hapmap]
rs10251985	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10259650	0.82[GIH][hapmap]
rs11769863	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11769941	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]
rs12155411	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1990363	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2037602	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2079849	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2534597	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2534598	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2534599	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4295563	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4339535	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4720271	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6462816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6973458	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6973870	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs756392	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7778240	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7778377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7787991	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7803902	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
12	esv3367303	chr7:38234691-38234869	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1990362	STARD3NL	cis	parietal	SCAN
rs1990362	VPS41	cis	cerebellum	SCAN

Chromatin state (count:72 , 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	chr7:38220200-38235400	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr7:38220200-38235400	Weak transcription	Thymus	Thymus
5	chr7:38220200-38236800	Weak transcription	Fetal Stomach	stomach
6	chr7:38220200-38246600	Weak transcription	Fetal Thymus	thymus
7	chr7:38220200-38254800	Weak transcription	Brain Hippocampus Middle	brain
8	chr7:38220400-38247000	Weak transcription	Fetal Intestine Small	intestine
9	chr7:38221000-38236400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr7:38221000-38246800	Weak transcription	Primary T cells from cord blood	blood
11	chr7:38223600-38255600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr7:38224200-38235800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr7:38224200-38235800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr7:38224200-38235800	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr7:38225000-38247000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr7:38225600-38235800	Weak transcription	Ovary	ovary
17	chr7:38225800-38235800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr7:38227000-38235400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:38227000-38235400	Weak transcription	NHLF	lung
20	chr7:38227000-38237400	Weak transcription	Aorta	Aorta
21	chr7:38227600-38238400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr7:38228000-38235400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr7:38228000-38236800	Weak transcription	Left Ventricle	heart
24	chr7:38228000-38256600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:38228200-38237400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr7:38228200-38237400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr7:38228200-38239400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr7:38228200-38241400	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr7:38228200-38254400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr7:38228800-38235800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr7:38228800-38239600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr7:38228800-38247200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr7:38229000-38236800	Weak transcription	Fetal Heart	heart
34	chr7:38229200-38249200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr7:38229600-38246600	Weak transcription	Primary B cells from cord blood	blood
36	chr7:38229800-38237400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr7:38229800-38246400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr7:38230200-38235000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr7:38230200-38235200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr7:38230200-38235200	Weak transcription	HSMMtube	muscle
41	chr7:38230200-38235400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr7:38230200-38235400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr7:38230200-38235400	Weak transcription	NH-A	brain
44	chr7:38230200-38235400	Weak transcription	NHEK	skin
45	chr7:38230200-38235400	Weak transcription	Osteobl	bone
46	chr7:38230200-38259200	Weak transcription	K562	blood
47	chr7:38230400-38235200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr7:38230400-38235400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr7:38230400-38235400	Weak transcription	HMEC	breast
50	chr7:38230600-38235400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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