Variant report

Variant	rs10175234
Chromosome Location	chr2:113037920-113037921
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10167090	0.91[ASN][1000 genomes]
rs10169159	0.91[ASN][1000 genomes]
rs10177573	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10183121	0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs10191002	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10203614	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10205038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10205897	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10211300	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs10439391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10864903	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11123132	0.94[CHB][hapmap];1.00[YRI][hapmap]
rs11123135	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11674953	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs11688418	0.90[ASN][1000 genomes]
rs11689487	0.90[ASN][1000 genomes]
rs11691431	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs11691794	0.90[ASN][1000 genomes]
rs11903741	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12711737	0.85[ASN][1000 genomes]
rs12711738	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12711739	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13387611	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34623958	0.91[ASN][1000 genomes]
rs4299347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4352239	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4392265	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4399734	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4419238	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4430968	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4446076	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4450606	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4456711	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4507112	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4522611	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4525706	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4542853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4578863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4622729	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4630773	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4849056	0.83[ASN][1000 genomes]
rs4849057	0.84[ASN][1000 genomes]
rs4849058	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62160223	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6542045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6542048	0.94[ASN][1000 genomes]
rs6542050	0.95[ASN][1000 genomes]
rs6542051	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6542054	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6706874	0.82[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6716010	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6725933	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6733138	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6745942	0.95[ASN][1000 genomes]
rs6751146	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6758110	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6761599	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs71414636	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72831684	0.95[ASN][1000 genomes]
rs7557281	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7557862	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7571435	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7591439	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7598168	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7600338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7601200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7601888	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv582703	chr2:112920219-113100014	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv874867	chr2:112930064-113038409	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv1805614	chr2:112949713-113048705	Enhancers Flanking Active TSS 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	36 gene(s)	inside rSNPs	diseases
8	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv874868	chr2:113021811-113076095	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv874869	chr2:113021811-113089267	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	nsv874870	chr2:113021811-113097699	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	nsv874871	chr2:113021811-113217630	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
13	nsv874872	chr2:113027569-113070889	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
14	nsv874873	chr2:113027569-113083367	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
15	nsv874874	chr2:113027569-113089267	Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
16	nsv963704	chr2:113036252-113044944	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10175234	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs10175234	RGPD8	cis	Artery Tibial	GTEx
rs10175234	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs10175234	RGPD8	cis	lung	GTEx
rs10175234	RGPD8	cis	Nerve Tibial	GTEx
rs10175234	RGPD8	cis	Muscle Skeletal	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113034200-113058200	Weak transcription	Ovary	ovary
2	chr2:113034400-113047800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:113034400-113051400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:113034400-113097000	Weak transcription	Psoas Muscle	Psoas
5	chr2:113034600-113039600	Weak transcription	Fetal Heart	heart
6	chr2:113034800-113039600	Weak transcription	HepG2	liver
7	chr2:113034800-113041400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr2:113035000-113046000	Weak transcription	Fetal Kidney	kidney
9	chr2:113035000-113057800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:113035000-113057800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:113035000-113057800	Weak transcription	Fetal Intestine Small	intestine
12	chr2:113035200-113040200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:113035400-113040600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:113035400-113047600	Weak transcription	Osteobl	bone
15	chr2:113035600-113040400	Weak transcription	Brain Anterior Caudate	brain
16	chr2:113035600-113041200	Weak transcription	K562	blood
17	chr2:113035600-113047600	Weak transcription	NHDF-Ad	bronchial
18	chr2:113035600-113058200	Weak transcription	Primary B cells from cord blood	blood
19	chr2:113035800-113038000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:113035800-113040200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:113035800-113058000	Weak transcription	Primary T cells from cord blood	blood
22	chr2:113035800-113060400	Weak transcription	Fetal Thymus	thymus
23	chr2:113035800-113067400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:113036000-113040000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:113036000-113040000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr2:113036000-113040600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:113036200-113041200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:113036600-113040000	Weak transcription	Liver	Liver
29	chr2:113036600-113058000	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr2:113037000-113040000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr2:113037000-113054200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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