Variant report

Variant	rs12043604
Chromosome Location	chr1:85919560-85919561
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85917225..85920485-chr1:85926526..85929082,3	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12021849	0.84[EUR][1000 genomes]
rs12022443	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12022538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023006	0.85[ASN][1000 genomes]
rs12023795	0.84[EUR][1000 genomes]
rs12024405	0.85[ASN][1000 genomes]
rs12024508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12029474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12029684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12033170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12033315	0.84[EUR][1000 genomes]
rs12033473	0.85[ASN][1000 genomes]
rs12034206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12034481	0.90[ASN][1000 genomes]
rs12036146	0.85[ASN][1000 genomes]
rs12038279	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12039188	0.85[ASN][1000 genomes]
rs12041140	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12042485	0.85[ASN][1000 genomes]
rs12043505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12045545	0.85[ASN][1000 genomes]
rs12046433	0.85[ASN][1000 genomes]
rs12047139	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12047220	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12048263	0.85[ASN][1000 genomes]
rs12049582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1851782	0.84[EUR][1000 genomes]
rs2300638	0.85[ASN][1000 genomes]
rs28847138	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3813603	0.85[ASN][1000 genomes]
rs485987	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs551786	0.84[EUR][1000 genomes]
rs58489234	0.83[ASN][1000 genomes]
rs61164145	0.84[EUR][1000 genomes]
rs74098846	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 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	chr1:85901400-85923000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:85907000-85919600	Weak transcription	Right Atrium	heart
3	chr1:85913800-85920400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:85914200-85924800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:85915200-85919600	Weak transcription	Aorta	Aorta
6	chr1:85915200-85927800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:85915600-85920200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:85915600-85925400	Weak transcription	Brain Germinal Matrix	brain
9	chr1:85915800-85920600	Weak transcription	Small Intestine	intestine
10	chr1:85916400-85920200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:85916400-85921800	Enhancers	Liver	Liver
12	chr1:85916600-85920000	Genic enhancers	Osteobl	bone
13	chr1:85917000-85922200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:85917000-85923000	Weak transcription	Psoas Muscle	Psoas
15	chr1:85917200-85920000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:85917400-85919600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:85917400-85919600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:85917400-85919600	Weak transcription	Lung	lung
19	chr1:85917400-85919600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:85917400-85920000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr1:85917400-85922400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:85917400-85926400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:85917400-85929400	Weak transcription	Fetal Muscle Leg	muscle
24	chr1:85917400-85929400	Weak transcription	Gastric	stomach
25	chr1:85917400-85929800	Weak transcription	Esophagus	oesophagus
26	chr1:85917600-85921600	Enhancers	Fetal Lung	lung
27	chr1:85917800-85919600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:85917800-85927200	Weak transcription	NH-A	brain
29	chr1:85917800-85928800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:85918200-85920600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:85918200-85921400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:85918400-85919800	Enhancers	Rectal Smooth Muscle	rectum
33	chr1:85918400-85920000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:85918400-85920000	Enhancers	Fetal Intestine Large	intestine
35	chr1:85918400-85920200	Enhancers	Fetal Intestine Small	intestine
36	chr1:85918400-85920800	Enhancers	Colon Smooth Muscle	Colon
37	chr1:85918600-85920000	Enhancers	NHDF-Ad	bronchial
38	chr1:85918600-85920200	Enhancers	Ovary	ovary
39	chr1:85918600-85920200	Genic enhancers	HSMM	muscle
40	chr1:85918600-85920800	Enhancers	Fetal Stomach	stomach
41	chr1:85918800-85919600	Enhancers	Fetal Brain Female	brain
42	chr1:85918800-85919800	Enhancers	Adipose Nuclei	Adipose
43	chr1:85918800-85920200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:85918800-85920600	Enhancers	Muscle Satellite Cultured Cells	--
45	chr1:85918800-85920600	Enhancers	HepG2	liver
46	chr1:85918800-85923600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr1:85919000-85920000	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr1:85919000-85920200	Enhancers	Pancreas	Pancrea
49	chr1:85919000-85920400	Enhancers	NHLF	lung
50	chr1:85919000-85920800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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