Variant report

Variant	rs6485596
Chromosome Location	chr11:45184331-45184332
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:45167897..45170381-chr11:45182910..45186280,3	MCF-7	breast:
2	chr11:45176255..45180138-chr11:45180420..45184771,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000019485	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10742743	0.85[JPT][hapmap]
rs10742744	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10742745	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10742746	0.89[ASN][1000 genomes]
rs1078930	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10838425	0.85[JPT][hapmap]
rs10838426	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11038356	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11038361	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12281438	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2863159	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3758722	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3758728	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3781706	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4755948	0.95[EUR][1000 genomes]
rs4755953	0.85[JPT][hapmap]
rs6416128	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6485594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6485595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6485597	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6485598	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6485599	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6485601	0.95[EUR][1000 genomes]
rs6485602	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs746555	0.95[EUR][1000 genomes]
rs7937949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7942214	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7942347	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7945018	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv825852	chr11:45141386-45228580	Bivalent/Poised TSS Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv541025	chr11:45154352-45193352	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	nsv1048493	chr11:45166054-45205695	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45169800-45188000	Weak transcription	Primary T cells from cord blood	blood
2	chr11:45170000-45190000	Weak transcription	Primary B cells from cord blood	blood
3	chr11:45170400-45185200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr11:45172400-45190000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:45175600-45186200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr11:45176000-45186600	Genic enhancers	Fetal Stomach	stomach
7	chr11:45178200-45187600	Enhancers	Fetal Heart	heart
8	chr11:45178400-45185200	Enhancers	Fetal Muscle Leg	muscle
9	chr11:45178800-45186800	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr11:45179400-45184800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr11:45180000-45185000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr11:45180000-45193000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr11:45180200-45185400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr11:45180200-45185600	Weak transcription	HMEC	breast
15	chr11:45180400-45184600	Weak transcription	Fetal Brain Male	brain
16	chr11:45180400-45185000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr11:45180600-45185800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr11:45180800-45184600	Weak transcription	HSMMtube	muscle
19	chr11:45180800-45185200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr11:45181600-45193600	Weak transcription	Fetal Intestine Large	intestine
21	chr11:45182000-45187200	Enhancers	Brain Angular Gyrus	brain
22	chr11:45182200-45184600	Enhancers	Colon Smooth Muscle	Colon
23	chr11:45182200-45185800	Enhancers	Lung	lung
24	chr11:45182200-45186600	Enhancers	Fetal Muscle Trunk	muscle
25	chr11:45182200-45186800	Enhancers	Brain Hippocampus Middle	brain
26	chr11:45182200-45187200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr11:45182400-45185600	Enhancers	Spleen	Spleen
28	chr11:45182400-45186400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr11:45182400-45187000	Enhancers	Right Ventricle	heart
30	chr11:45182400-45187400	Enhancers	Ovary	ovary
31	chr11:45182600-45184800	Enhancers	Pancreas	Pancrea
32	chr11:45182800-45184400	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr11:45182800-45184600	Enhancers	Psoas Muscle	Psoas
34	chr11:45182800-45185000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:45183000-45186800	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr11:45183200-45186600	Enhancers	Fetal Brain Female	brain
37	chr11:45183600-45185800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:45183600-45186600	Enhancers	Brain Germinal Matrix	brain
39	chr11:45183600-45186800	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr11:45183600-45200400	Weak transcription	Esophagus	oesophagus
41	chr11:45183800-45185000	Weak transcription	Aorta	Aorta
42	chr11:45183800-45185400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr11:45183800-45185600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr11:45183800-45185800	Enhancers	Stomach Smooth Muscle	stomach
45	chr11:45183800-45186200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr11:45183800-45187400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr11:45183800-45188200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr11:45183800-45190400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr11:45183800-45190800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr11:45183800-45201200	Weak transcription	Gastric	stomach

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