Variant report

Variant	rs10913977
Chromosome Location	chr1:180356816-180356817
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:180354979..180356991-chr1:180360915..180363474,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10494526	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10913960	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10913962	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10913963	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10913964	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10913967	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10913975	1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10914021	1.00[JPT][hapmap]
rs10914022	0.93[JPT][hapmap]
rs12022629	1.00[EUR][1000 genomes]
rs12037744	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12069143	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12089448	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12403226	0.83[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs12404700	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12407684	0.87[JPT][hapmap]
rs12409923	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2025593	0.94[ASN][1000 genomes]
rs2877481	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36088499	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6425646	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6684596	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs878641	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs912766	1.00[CHB][hapmap];0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv527918	chr1:180279710-180443808	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013716	chr1:180287338-180477072	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
5	nsv535221	chr1:180287338-180477072	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
6	esv2762200	chr1:180300936-180493841	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
7	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
8	nsv1009742	chr1:180342203-180385459	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180341200-180401400	Weak transcription	Osteobl	bone
2	chr1:180348200-180382600	Weak transcription	Pancreas	Pancrea
3	chr1:180349400-180364200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:180349400-180407000	Weak transcription	Esophagus	oesophagus
5	chr1:180351600-180378400	Weak transcription	HSMM	muscle
6	chr1:180352400-180381400	Weak transcription	Hela-S3	cervix
7	chr1:180352800-180399400	Weak transcription	Fetal Thymus	thymus
8	chr1:180353800-180357000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:180354200-180364200	Weak transcription	NH-A	brain
10	chr1:180354600-180374000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:180354800-180358600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:180354800-180386600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:180355000-180360600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr1:180355200-180357000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:180355200-180364800	Weak transcription	K562	blood
16	chr1:180355200-180402600	Weak transcription	HMEC	breast
17	chr1:180355400-180361200	Weak transcription	Small Intestine	intestine
18	chr1:180355400-180378800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:180355600-180378400	Weak transcription	Placenta	Placenta
20	chr1:180355600-180390800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:180356000-180357000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:180356200-180357000	Strong transcription	Primary B cells from cord blood	blood
23	chr1:180356200-180357000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr1:180356200-180357000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:180356200-180357000	Strong transcription	Fetal Intestine Large	intestine
26	chr1:180356200-180357000	ZNF genes & repeats	Ovary	ovary
27	chr1:180356200-180357000	Strong transcription	A549	lung
28	chr1:180356400-180357000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:180356400-180357000	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr1:180356400-180357000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:180356400-180357000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:180356400-180357000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
33	chr1:180356400-180357000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:180356400-180357000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:180356400-180357000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:180356400-180357000	ZNF genes & repeats	Fetal Lung	lung
37	chr1:180356400-180357000	ZNF genes & repeats	Dnd41	blood
38	chr1:180356400-180363800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:180356600-180364200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:180356600-180364200	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:180356600-180381400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:180356600-180394000	Weak transcription	NHDF-Ad	bronchial
43	chr1:180356800-180357000	Flanking Active TSS	GM12878-XiMat	blood
44	chr1:180356800-180363600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:180356800-180364200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:180356800-180364800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:180356800-180373000	Weak transcription	Fetal Intestine Small	intestine
48	chr1:180356800-180378600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:180356800-180378800	Weak transcription	Left Ventricle	heart
50	chr1:180356800-180380800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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