Variant report

Variant	rs62413390
Chromosome Location	chr6:80284245-80284246
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SH3BGRL2-5	chr6:80283594-80285247	NONHSAT113706

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10498921	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1158770	1.00[ASN][1000 genomes]
rs1158771	1.00[ASN][1000 genomes]
rs11965020	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966497	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1485370	0.84[ASN][1000 genomes]
rs1485372	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504368	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16890774	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890835	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890850	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890862	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890875	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17335231	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17727505	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2575204	1.00[ASN][1000 genomes]
rs2575208	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655666	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655677	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655679	0.86[ASN][1000 genomes]
rs2655680	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655703	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2803188	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2803189	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2803197	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269343	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55830218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55989614	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56087572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56745436	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61152095	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411332	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411348	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413360	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413362	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62413366	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413368	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413370	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413371	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62413372	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413377	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413380	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413382	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413395	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413399	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62413401	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62413416	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62413421	0.92[AMR][1000 genomes]
rs6454124	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6454125	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6907133	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917186	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6920635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921102	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934060	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73747413	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73750727	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7745158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7749776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763266	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763268	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768651	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768724	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769778	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7772722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775232	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs992872	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv886301	chr6:80111104-80339088	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv886302	chr6:80111104-80355973	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1027388	chr6:80113449-80355973	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv830707	chr6:80134625-80325171	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1029259	chr6:80142754-80340332	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv463906	chr6:80240951-80313297	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv604052	chr6:80240951-80313297	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1018318	chr6:80241029-80465282	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80278000-80287400	Weak transcription	Small Intestine	intestine
2	chr6:80279400-80287600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:80279800-80284600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:80280600-80284600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:80280800-80285200	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr6:80281000-80284400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:80281000-80284400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:80281000-80284400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:80281000-80284400	Weak transcription	HMEC	breast
10	chr6:80281000-80284400	Weak transcription	NHEK	skin
11	chr6:80281000-80284800	Weak transcription	Ovary	ovary
12	chr6:80281000-80309600	Weak transcription	Brain Angular Gyrus	brain
13	chr6:80281200-80287400	Weak transcription	Fetal Intestine Small	intestine
14	chr6:80281200-80289600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:80282000-80284400	Weak transcription	Stomach Mucosa	stomach
16	chr6:80282600-80284800	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr6:80283000-80285000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:80283200-80284800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:80283400-80285000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr6:80283400-80285000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr6:80283400-80285000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr6:80283600-80285000	Enhancers	HepG2	liver
23	chr6:80283600-80285000	Enhancers	NH-A	brain
24	chr6:80283800-80284800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr6:80283800-80284800	Enhancers	H9 Cell Line	embryonic stem cell
26	chr6:80283800-80284800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:80283800-80285000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:80283800-80285000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:80283800-80285000	Enhancers	Muscle Satellite Cultured Cells	--
30	chr6:80283800-80285000	Enhancers	HSMM	muscle
31	chr6:80283800-80285000	Enhancers	HUVEC	blood vessel
32	chr6:80284000-80284800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:80284000-80284800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:80284000-80284800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:80284000-80284800	Enhancers	NHDF-Ad	bronchial
36	chr6:80284000-80284800	Enhancers	Osteobl	bone
37	chr6:80284000-80285000	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr6:80284000-80285200	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr6:80284200-80284800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr6:80284200-80284800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:80284200-80284800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links