Variant report

Variant	rs7661194
Chromosome Location	chr4:57872421-57872422
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10866440	1.00[JPT][hapmap]
rs10866441	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1105434	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1107675	1.00[JPT][hapmap]
rs11727683	0.88[ASN][1000 genomes]
rs11730321	0.93[JPT][hapmap]
rs11732394	0.91[CEU][hapmap]
rs11735158	0.81[ASN][1000 genomes]
rs11736869	0.83[CHB][hapmap]
rs11932673	1.00[JPT][hapmap]
rs12500454	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12511020	0.81[ASN][1000 genomes]
rs1277287	1.00[JPT][hapmap]
rs13108245	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs13125082	0.82[CEU][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap]
rs13146090	0.82[CEU][hapmap];0.88[GIH][hapmap];0.92[TSI][hapmap]
rs13146153	0.91[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs1625691	1.00[JPT][hapmap]
rs17081937	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs17087317	1.00[JPT][hapmap]
rs17087358	0.80[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap]
rs17087411	0.94[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs17087414	0.94[CHB][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs1713994	0.81[ASN][1000 genomes]
rs1718839	1.00[JPT][hapmap]
rs1877669	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2228991	1.00[JPT][hapmap]
rs2271808	0.80[CEU][hapmap];0.84[MEX][hapmap]
rs2412773	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3000	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs34855462	0.88[EUR][1000 genomes]
rs34948796	0.88[EUR][1000 genomes]
rs3733306	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs3796528	1.00[JPT][hapmap]
rs3806745	1.00[JPT][hapmap]
rs41495551	1.00[GIH][hapmap];0.83[TSI][hapmap]
rs41552420	0.86[ASN][1000 genomes]
rs41556916	0.88[ASN][1000 genomes]
rs56182208	0.88[ASN][1000 genomes]
rs56285301	0.88[ASN][1000 genomes]
rs57469512	0.88[ASN][1000 genomes]
rs62310298	0.88[EUR][1000 genomes]
rs6554398	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs67541678	0.88[EUR][1000 genomes]
rs6838948	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6847086	0.82[JPT][hapmap]
rs6852110	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs73242631	0.86[ASN][1000 genomes]
rs7680734	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs781666	1.00[JPT][hapmap]
rs781668	1.00[JPT][hapmap]
rs9055	0.82[CEU][hapmap]
rs9942208	1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7661194	RP11-738E22.3	cis	Skin Sun Exposed Lower leg	GTEx
rs7661194	TXNDC9	cis	parietal	SCAN
rs7661194	POLR2B	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57846000-57881000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:57846800-57900000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:57848400-57875200	Weak transcription	Stomach Mucosa	stomach
4	chr4:57848600-57900000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr4:57849000-57900000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:57849200-57886200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:57849600-57884600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr4:57850600-57899400	Strong transcription	Fetal Thymus	thymus
9	chr4:57850800-57899400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:57851000-57899200	Strong transcription	Primary T cells from cord blood	blood
11	chr4:57851000-57899400	Strong transcription	Duodenum Mucosa	Duodenum
12	chr4:57851200-57897200	Strong transcription	Fetal Intestine Large	intestine
13	chr4:57851400-57894800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:57851600-57899400	Strong transcription	Placenta	Placenta
15	chr4:57851800-57899400	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:57851800-57899400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr4:57851800-57899400	Strong transcription	Liver	Liver
18	chr4:57851800-57899600	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:57852000-57892200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr4:57852000-57894800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr4:57852000-57898200	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr4:57852200-57899000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr4:57852200-57899400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr4:57852600-57899400	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr4:57856000-57899400	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr4:57856200-57886200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:57856800-57900000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr4:57858200-57899800	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr4:57858400-57899800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:57858400-57899800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:57859000-57898000	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr4:57859400-57898600	Strong transcription	Dnd41	blood
33	chr4:57859600-57881800	Strong transcription	Primary B cells from cord blood	blood
34	chr4:57859600-57897800	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr4:57860200-57885000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr4:57860200-57898800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:57860600-57892800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr4:57861000-57881000	Weak transcription	Hela-S3	cervix
39	chr4:57861400-57884400	Strong transcription	Thymus	Thymus
40	chr4:57861400-57895000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr4:57862200-57873200	Weak transcription	Psoas Muscle	Psoas
42	chr4:57862200-57874600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr4:57862200-57875400	Weak transcription	Aorta	Aorta
44	chr4:57862200-57884400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:57862200-57891600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr4:57862200-57899400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr4:57862200-57900000	Strong transcription	Fetal Muscle Leg	muscle
48	chr4:57862400-57879600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:57862400-57883200	Weak transcription	Fetal Heart	heart
50	chr4:57862400-57886400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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