Variant report

Variant	rs934083
Chromosome Location	chr3:54790379-54790380
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1008187	0.83[ASW][hapmap]
rs10865989	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130431	0.82[ASW][hapmap];0.88[YRI][hapmap]
rs11707823	0.87[ASN][1000 genomes]
rs11711913	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1346407	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1559999	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2360021	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2360026	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3732748	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4353779	0.82[CHB][hapmap]
rs4384925	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.85[ASN][1000 genomes]
rs4563383	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs515920	0.95[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs517729	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs521694	0.80[ASN][1000 genomes]
rs550210	0.83[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap]
rs578032	0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs583190	0.85[CEU][hapmap];0.95[CHB][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs589281	0.83[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.80[ASN][1000 genomes]
rs652424	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6809466	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7636321	0.85[CEU][hapmap]
rs838022	0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]

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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54784600-54797200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr3:54785200-54793800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:54785800-54798200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:54787400-54792800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:54787400-54800200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:54787600-54790600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:54787600-54804600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:54788800-54792600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:54789000-54791800	Enhancers	NHLF	lung
10	chr3:54789200-54790600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:54789400-54791000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:54789400-54791000	Enhancers	Osteobl	bone
13	chr3:54789400-54791400	Enhancers	NHDF-Ad	bronchial
14	chr3:54789400-54793800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:54789800-54790400	Enhancers	Colon Smooth Muscle	Colon
16	chr3:54789800-54791400	Enhancers	NH-A	brain
17	chr3:54790000-54794400	Enhancers	Fetal Stomach	stomach
18	chr3:54790200-54790600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:54790200-54790600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:54790200-54790800	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr3:54790200-54790800	Enhancers	Fetal Kidney	kidney
22	chr3:54790200-54790800	Enhancers	Fetal Muscle Leg	muscle
23	chr3:54790200-54791000	Enhancers	Rectal Smooth Muscle	rectum
24	chr3:54790200-54791200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:54790200-54791400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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