Variant report

Variant	rs12549996
Chromosome Location	chr8:48418206-48418207
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:48416787..48427648-chr8:48644938..48653304,27	MCF-7	breast:
2	chr8:48417772..48429044-chr8:48646094..48652486,42	MCF-7	breast:
3	chr8:48417465..48419958-chr8:48587324..48588844,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221869	Chromatin interaction
ENSG00000164808	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10094128	0.83[CEU][hapmap]
rs1038797	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs10808752	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs10957549	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10957644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10958058	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1106607	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11778548	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11781727	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs11782572	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11784823	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12544329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12547513	0.83[ASN][1000 genomes]
rs12675378	0.98[EUR][1000 genomes]
rs12678110	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12682269	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs13259913	0.84[ASN][1000 genomes]
rs16928696	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1872840	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2087656	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2129617	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2129618	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2130412	0.97[EUR][1000 genomes]
rs2130413	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2172121	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs4489323	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4536257	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs4594029	0.82[CEU][hapmap]
rs4608108	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4873102	0.95[JPT][hapmap]
rs4873368	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs4873395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4873399	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4873437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4873478	0.83[CEU][hapmap]
rs4873507	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4873529	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4873546	0.81[CEU][hapmap]
rs4873565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4873619	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55941013	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56092229	0.94[EUR][1000 genomes]
rs62539116	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62539144	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62539147	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62539150	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6982620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6986054	0.82[CEU][hapmap]
rs6987043	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6989917	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6990123	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs7012341	0.81[ASN][1000 genomes]
rs7826284	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs7842068	0.82[CEU][hapmap]
rs876915	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs923499	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693377	chr8:47824261-48582964	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv491863	chr8:48053825-48586176	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1025674	chr8:48306843-48548862	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1023409	chr8:48320442-48454089	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv539595	chr8:48320442-48454089	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv890848	chr8:48405007-48535622	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv470211	chr8:48405007-48545961	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 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	chr8:48394200-48419800	Weak transcription	Pancreas	Pancrea
2	chr8:48397600-48419400	Weak transcription	Primary T cells from cord blood	blood
3	chr8:48397600-48426400	Weak transcription	Aorta	Aorta
4	chr8:48398200-48420000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr8:48398200-48421600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr8:48398800-48423400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr8:48404800-48421200	Weak transcription	Lung	lung
8	chr8:48407800-48418600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr8:48410600-48420800	Weak transcription	Brain Hippocampus Middle	brain
10	chr8:48410600-48424000	Weak transcription	Brain Angular Gyrus	brain
11	chr8:48410800-48421600	Weak transcription	HSMM	muscle
12	chr8:48411000-48420600	Weak transcription	Fetal Brain Male	brain
13	chr8:48411400-48420000	Weak transcription	HMEC	breast
14	chr8:48411600-48424000	Weak transcription	Fetal Kidney	kidney
15	chr8:48411800-48419800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr8:48411800-48420600	Weak transcription	Colon Smooth Muscle	Colon
17	chr8:48411800-48423400	Weak transcription	A549	lung
18	chr8:48411800-48423400	Weak transcription	Hela-S3	cervix
19	chr8:48411800-48423800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr8:48412000-48419600	Weak transcription	HSMMtube	muscle
21	chr8:48412000-48421600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr8:48412000-48421600	Weak transcription	Fetal Lung	lung
23	chr8:48416000-48419800	Weak transcription	Left Ventricle	heart
24	chr8:48416800-48421800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr8:48416800-48423800	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr8:48417400-48418400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr8:48417400-48418400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr8:48417400-48418400	ZNF genes & repeats	Fetal Stomach	stomach
29	chr8:48417400-48418400	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr8:48417400-48418800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr8:48417600-48418400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr8:48417600-48418400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr8:48417600-48418600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
34	chr8:48417600-48418800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
35	chr8:48417600-48419400	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr8:48417800-48419400	Weak transcription	Spleen	Spleen
37	chr8:48418200-48418400	ZNF genes & repeats	Fetal Muscle Leg	muscle
38	chr8:48418200-48418800	ZNF genes & repeats	Dnd41	blood
39	chr8:48418200-48419400	Enhancers	Primary B cells from cord blood	blood
40	chr8:48418200-48419400	Weak transcription	Gastric	stomach
41	chr8:48418200-48419800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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