Variant report

Variant	rs2656953
Chromosome Location	chr5:89786766-89786767
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10942595	0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11750517	0.88[JPT][hapmap]
rs1544958	0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2115500	0.85[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2247158	0.91[MEX][hapmap]
rs2366768	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs250376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562515	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2562516	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2562517	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2562518	0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2562519	0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2562520	0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs27601	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs27658	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2914672	0.85[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2938788	0.92[ASN][1000 genomes]
rs2963698	0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs37480	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs3805480	0.86[JPT][hapmap]
rs3933063	0.92[ASN][1000 genomes]
rs40204	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6894539	0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7712322	0.87[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7722900	0.86[JPT][hapmap];0.90[MEX][hapmap]
rs7726781	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv882364	chr5:89748142-89808531	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2656953	GPR98	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89771200-89788600	Weak transcription	Psoas Muscle	Psoas
2	chr5:89771200-89796200	Weak transcription	Fetal Intestine Small	intestine
3	chr5:89771600-89798800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:89771600-89814400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr5:89773400-89795600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:89773600-89798800	Weak transcription	HMEC	breast
7	chr5:89773800-89816000	Weak transcription	HepG2	liver
8	chr5:89773800-89824400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:89774000-89787600	Weak transcription	Brain Hippocampus Middle	brain
10	chr5:89774000-89814600	Weak transcription	Dnd41	blood
11	chr5:89774400-89814600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:89775000-89789800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:89776200-89789800	Weak transcription	GM12878-XiMat	blood
14	chr5:89776200-89799200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:89776200-89800400	Weak transcription	HUVEC	blood vessel
16	chr5:89776600-89798800	Weak transcription	NHEK	skin
17	chr5:89777000-89806600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:89780400-89799800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:89780400-89810800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:89780600-89787600	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr5:89780600-89822600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr5:89780800-89800000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:89780800-89800400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr5:89781000-89799400	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr5:89781200-89793600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr5:89783000-89790000	Weak transcription	K562	blood
27	chr5:89783000-89800800	Weak transcription	A549	lung
28	chr5:89783800-89813400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:89784600-89795600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:89784800-89791000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr5:89784800-89814600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr5:89785000-89790800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:89785200-89786800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:89785200-89787400	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr5:89785200-89798800	Weak transcription	NHDF-Ad	bronchial
36	chr5:89785400-89798800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr5:89785400-89799400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr5:89785400-89814600	Weak transcription	NHLF	lung
39	chr5:89786200-89799400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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