Variant report

Variant	rs6687388
Chromosome Location	chr1:95515124-95515125
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1023330	0.84[CHB][hapmap]
rs10493880	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10735790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10782996	0.92[ASN][1000 genomes]
rs10874902	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165299	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11585462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11591183	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12563592	0.81[EUR][1000 genomes]
rs12569038	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12569207	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12741128	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12748237	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12751774	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2298162	0.83[JPT][hapmap]
rs2391388	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2391389	0.91[ASN][1000 genomes]
rs2766010	0.96[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2766011	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2797616	0.83[AMR][1000 genomes]
rs2797622	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2893274	0.84[ASN][1000 genomes]
rs34280926	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35678413	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35888232	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4259714	0.84[ASN][1000 genomes]
rs4309032	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4339907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4390223	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4630159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4847220	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4949965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4950056	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4950057	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4950058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4950077	0.92[CHB][hapmap]
rs61774262	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6675668	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6683112	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6687450	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6698046	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7533303	0.81[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap]
rs7537374	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7539139	0.91[ASN][1000 genomes]
rs7547662	0.82[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs9437665	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9437672	0.96[ASN][1000 genomes]
rs9437689	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9437810	0.96[ASN][1000 genomes]
rs9437812	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9437813	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9661031	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	nsv830636	chr1:95495849-95703126	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv3402740	chr1:95500980-95527860	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95488200-95537600	Weak transcription	Right Ventricle	heart
2	chr1:95489400-95517200	Weak transcription	Aorta	Aorta
3	chr1:95491600-95529600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:95505600-95537400	Weak transcription	Right Atrium	heart
5	chr1:95506000-95517000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:95506000-95537800	Weak transcription	Pancreas	Pancrea
7	chr1:95506600-95527800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:95509000-95528000	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:95509200-95525600	Weak transcription	Adipose Nuclei	Adipose
10	chr1:95509400-95515800	Weak transcription	Brain Anterior Caudate	brain
11	chr1:95509400-95527600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:95509400-95532800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:95509400-95534200	Weak transcription	Fetal Intestine Small	intestine
14	chr1:95509600-95526400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:95513800-95515600	Enhancers	Liver	Liver
16	chr1:95514200-95527400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:95514400-95527800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:95514600-95515600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:95514600-95530200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:95515000-95518200	Weak transcription	Ovary	ovary

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