Variant report

Variant	rs1550931
Chromosome Location	chr4:87809387-87809388
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC10A6-2	chr4:87809293-87809424	NONHSAT097286

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10017360	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11731586	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11935015	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11939730	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12503661	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13128982	0.91[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs13137142	0.88[ASN][1000 genomes]
rs13141097	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1374934	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1584345	0.91[GIH][hapmap];0.82[MEX][hapmap]
rs2594281	0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2594282	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2594284	0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2705622	1.00[ASN][1000 genomes]
rs2705623	0.95[ASN][1000 genomes]
rs2705624	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2705626	0.89[ASN][1000 genomes]
rs2705627	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2904149	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2922234	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4508849	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs4693788	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4693789	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56414102	0.87[ASN][1000 genomes]
rs57477100	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6531936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.88[ASN][1000 genomes]
rs6531937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.88[ASN][1000 genomes]
rs73838351	0.88[ASN][1000 genomes]
rs7656537	0.86[ASN][1000 genomes]
rs7657443	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7663218	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs8180256	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv508297	chr4:87778783-87868508	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87801600-87811800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:87803200-87811800	Weak transcription	NHEK	skin
3	chr4:87804200-87812600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr4:87806800-87811800	Weak transcription	Fetal Lung	lung
5	chr4:87806800-87812000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:87806800-87812600	Weak transcription	Adipose Nuclei	Adipose
7	chr4:87806800-87813000	Weak transcription	Left Ventricle	heart
8	chr4:87807200-87812800	Weak transcription	Brain Anterior Caudate	brain
9	chr4:87807600-87811000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:87808200-87811800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:87808200-87811800	Weak transcription	Pancreas	Pancrea
12	chr4:87808200-87812000	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:87808200-87812200	Weak transcription	Fetal Intestine Large	intestine
14	chr4:87808200-87812600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:87808600-87809400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:87808600-87812200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr4:87809200-87809600	Weak transcription	Esophagus	oesophagus
18	chr4:87809200-87810800	Enhancers	HUVEC	blood vessel
19	chr4:87809200-87811800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:87809200-87812000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:87809200-87812000	Weak transcription	Placenta	Placenta

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