Variant report

Variant	rs6878131
Chromosome Location	chr5:15646811-15646812
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10053108	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11745041	0.85[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.85[MEX][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11953541	0.85[CEU][hapmap]
rs12187518	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs12654662	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12656882	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12658046	0.92[CEU][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs12658048	0.81[EUR][1000 genomes]
rs12757	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs13159972	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13165880	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13170478	0.96[CEU][hapmap];0.81[GIH][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13185548	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1429032	0.88[CEU][hapmap]
rs1429033	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17523312	0.96[CEU][hapmap]
rs17647599	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17703964	0.83[CHB][hapmap];0.87[CHD][hapmap]
rs17703976	0.82[CHD][hapmap]
rs1835128	0.88[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap]
rs1835129	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs1991529	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2217346	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2914762	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs2914763	0.80[EUR][1000 genomes]
rs4295390	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4510586	0.81[CHD][hapmap]
rs4702087	0.87[CHB][hapmap]
rs4702090	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4702098	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58080135	0.83[ASN][1000 genomes]
rs6869226	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6873476	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6878081	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6891138	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6892081	0.82[CHD][hapmap]
rs6898779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7701322	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7704791	0.80[CHD][hapmap]
rs7720476	1.00[CEU][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv516929	chr5:15087791-15870300	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1023068	chr5:15095221-15863583	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv869040	chr5:15097602-15866117	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv530222	chr5:15151662-15851485	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv830214	chr5:15589809-15791032	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv3507774	chr5:15593461-15822407	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3507776	chr5:15593461-15822407	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1028089	chr5:15636285-15883910	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv537676	chr5:15636285-15883910	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1024248	chr5:15638067-15863583	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv537677	chr5:15638067-15863583	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15627600-15648000	Weak transcription	Fetal Muscle Leg	muscle
2	chr5:15638200-15647400	Weak transcription	Brain Angular Gyrus	brain
3	chr5:15638600-15647400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:15640600-15655600	Weak transcription	Brain Anterior Caudate	brain
5	chr5:15641400-15647400	Weak transcription	Fetal Stomach	stomach
6	chr5:15642600-15648400	Enhancers	Fetal Heart	heart
7	chr5:15644400-15655800	Weak transcription	Brain Substantia Nigra	brain
8	chr5:15644600-15647000	Enhancers	NHDF-Ad	bronchial
9	chr5:15644800-15648800	Enhancers	Left Ventricle	heart
10	chr5:15645200-15647800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr5:15645400-15648200	Enhancers	Aorta	Aorta
12	chr5:15645600-15647000	Enhancers	Ovary	ovary
13	chr5:15645600-15649000	Enhancers	HSMMtube	muscle
14	chr5:15645600-15649800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr5:15645800-15657600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:15646000-15647000	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr5:15646000-15654000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:15646200-15648000	Weak transcription	Right Atrium	heart
19	chr5:15646200-15649400	Enhancers	Dnd41	blood
20	chr5:15646200-15650000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr5:15646200-15650600	Weak transcription	HSMM	muscle
22	chr5:15646400-15647400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:15646600-15647000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr5:15646600-15647000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:15646600-15647000	Enhancers	Brain Hippocampus Middle	brain
26	chr5:15646600-15647400	Weak transcription	Right Ventricle	heart
27	chr5:15646600-15653000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr5:15646800-15647000	Enhancers	Stomach Smooth Muscle	stomach
29	chr5:15646800-15650400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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