Variant report

Variant	rs17544971
Chromosome Location	chr7:50699818-50699819
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:50699706..50701584-chr7:50708525..50710076,2	K562	blood:
2	chr7:50697685..50701045-chr7:50715068..50717759,3	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10486758	0.89[CHD][hapmap]
rs17152083	1.00[JPT][hapmap]
rs17449259	0.87[AMR][1000 genomes]
rs17544866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17545714	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17546034	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17546062	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17546146	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17546202	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17546223	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2190496	1.00[CHB][hapmap]
rs3819431	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4612291	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55716906	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55857758	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56037477	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60767324	0.97[ASN][1000 genomes]
rs6948959	1.00[CHB][hapmap]
rs73113031	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73113047	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73113061	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73113067	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73113068	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73113089	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73113093	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73113096	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73113099	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114804	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114807	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114809	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114873	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73114877	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73114878	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73114889	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73114899	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73114901	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7456111	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs956117	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1023228	chr7:50573214-50777634	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1032882	chr7:50611138-50775257	Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv538834	chr7:50611138-50775257	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv1031138	chr7:50651793-50814881	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17544971	VSTM2A	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50674200-50709800	Weak transcription	Esophagus	oesophagus
2	chr7:50682600-50700400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr7:50682600-50700400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr7:50682600-50704600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr7:50683000-50700400	Weak transcription	A549	lung
6	chr7:50683600-50700400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr7:50685200-50700800	Weak transcription	Osteobl	bone
8	chr7:50687400-50700600	Enhancers	Fetal Heart	heart
9	chr7:50688400-50700600	Weak transcription	K562	blood
10	chr7:50689200-50700400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr7:50693600-50700800	Weak transcription	NHDF-Ad	bronchial
12	chr7:50693600-50705400	Weak transcription	NH-A	brain
13	chr7:50694200-50729200	Weak transcription	Hela-S3	cervix
14	chr7:50694400-50700200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr7:50694600-50700200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr7:50694600-50700400	Weak transcription	Ovary	ovary
17	chr7:50694600-50700600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr7:50694600-50707800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:50694600-50708400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr7:50694800-50700400	Weak transcription	HUVEC	blood vessel
21	chr7:50694800-50700800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr7:50694800-50701000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr7:50695000-50700200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr7:50695000-50700200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr7:50695000-50700400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr7:50695000-50700800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:50695000-50701000	Enhancers	Left Ventricle	heart
28	chr7:50695000-50720600	Weak transcription	Primary T cells from cord blood	blood
29	chr7:50695200-50700200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr7:50695400-50700200	Weak transcription	Gastric	stomach
31	chr7:50695400-50700400	Weak transcription	Adipose Nuclei	Adipose
32	chr7:50695600-50716000	Weak transcription	Fetal Stomach	stomach
33	chr7:50695800-50701000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr7:50696000-50700000	Weak transcription	Placenta	Placenta
35	chr7:50696400-50700200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr7:50696400-50700400	Weak transcription	HepG2	liver
37	chr7:50696600-50700600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr7:50696800-50700000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr7:50696800-50700000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr7:50696800-50700800	Enhancers	Right Atrium	heart
41	chr7:50697000-50700800	Enhancers	Psoas Muscle	Psoas
42	chr7:50697400-50700000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr7:50697400-50700000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr7:50697400-50700200	Enhancers	Brain Hippocampus Middle	brain
45	chr7:50697600-50716600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr7:50697800-50700400	Weak transcription	HSMM	muscle
47	chr7:50697800-50716800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr7:50698000-50700400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr7:50698200-50708800	Weak transcription	HSMMtube	muscle
50	chr7:50698400-50700000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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