Variant report

Variant	rs9398971
Chromosome Location	chr6:131378927-131378928
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10457561	0.82[CEU][hapmap]
rs10457563	0.82[CEU][hapmap]
rs10872375	0.96[ASN][1000 genomes]
rs11154611	0.86[ASN][1000 genomes]
rs11760051	0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs12195366	0.82[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs12196734	0.81[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs12197829	0.91[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12203760	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214021	0.98[ASN][1000 genomes]
rs1569195	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17059954	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1976981	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2151068	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2178282	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28812545	0.99[ASN][1000 genomes]
rs4259270	0.99[ASN][1000 genomes]
rs4498389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62423583	0.85[ASN][1000 genomes]
rs6901548	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6902930	0.99[ASN][1000 genomes]
rs6903705	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6907809	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6916206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6921207	0.82[GIH][hapmap]
rs6921542	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926372	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6935560	0.84[LWK][hapmap]
rs7763960	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7770892	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321264	0.88[ASN][1000 genomes]
rs9372986	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9372987	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9372989	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs9375784	0.84[ASN][1000 genomes]
rs9375785	0.87[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs9375787	0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs9375788	0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs9375789	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs9375790	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs9375794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9375795	0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs9375796	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9375797	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388873	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs9388876	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9398967	0.91[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs9398969	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9398970	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398972	0.99[ASN][1000 genomes]
rs9398973	0.99[ASN][1000 genomes]
rs9402301	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9402306	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9402310	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs9402313	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9402314	0.98[ASN][1000 genomes]
rs9483210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9492790	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9492792	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951251	0.96[ASN][1000 genomes]
rs954919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9398971	EPB41L2	cis	multi-tissue	Pritchard

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131373400-131381400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:131375600-131380600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:131375800-131382400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:131376000-131382600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:131376200-131379200	Weak transcription	Osteobl	bone
6	chr6:131376400-131380600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:131376400-131380600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:131376400-131380600	Weak transcription	Fetal Stomach	stomach
9	chr6:131376400-131381800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:131376800-131380800	Weak transcription	NHLF	lung
11	chr6:131377000-131380600	Weak transcription	NHDF-Ad	bronchial
12	chr6:131377000-131381800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:131377200-131381600	Weak transcription	Fetal Intestine Small	intestine
14	chr6:131377200-131382600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:131377200-131382600	Weak transcription	Primary T cells from cord blood	blood
16	chr6:131377400-131380600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:131377400-131382400	Weak transcription	Fetal Intestine Large	intestine
18	chr6:131377400-131382600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:131377400-131382600	Weak transcription	Aorta	Aorta
20	chr6:131377600-131379200	ZNF genes & repeats	GM12878-XiMat	blood
21	chr6:131377800-131379800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:131378000-131380600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:131378200-131382200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr6:131378400-131379400	Enhancers	HepG2	liver
25	chr6:131378600-131379400	Weak transcription	A549	lung
26	chr6:131378600-131381000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:131378600-131381600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:131378600-131382400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:131378800-131379200	Enhancers	Brain Substantia Nigra	brain
30	chr6:131378800-131380000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:131378800-131380600	Weak transcription	Brain Anterior Caudate	brain
32	chr6:131378800-131381200	Weak transcription	Primary B cells from cord blood	blood

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