Variant report

Variant	rs12043505
Chromosome Location	chr1:85785099-85785100
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	chr1:85783416..85785101-chr1:85792646..85795360,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12022538	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12023006	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024405	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12029474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12029684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12033170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs12033473	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12034206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12034481	0.94[ASN][1000 genomes]
rs12036146	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038279	0.90[ASN][1000 genomes]
rs12039188	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12041140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12042485	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12043604	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12045545	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12046433	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12047139	0.81[ASN][1000 genomes]
rs12047220	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12048263	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12049582	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs2300638	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28847138	0.98[ASN][1000 genomes]
rs3813603	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485987	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap]
rs58489234	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	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	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85774600-85785200	Weak transcription	Liver	Liver
2	chr1:85774600-85785800	Weak transcription	Fetal Intestine Large	intestine
3	chr1:85774600-85787000	Weak transcription	Fetal Stomach	stomach
4	chr1:85774600-85794800	Weak transcription	Spleen	Spleen
5	chr1:85774800-85790400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:85774800-85790600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:85774800-85794200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:85777400-85786400	Enhancers	NHLF	lung
9	chr1:85778200-85790400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:85778400-85785600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:85778800-85786000	Enhancers	NHEK	skin
12	chr1:85778800-85788800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:85778800-85789600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:85779000-85785600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:85779600-85787400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:85780000-85791800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:85780000-85795800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:85780200-85790400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:85780200-85795800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr1:85780400-85788200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr1:85780400-85791600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:85780400-85793200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:85780400-85795800	Weak transcription	Gastric	stomach
24	chr1:85780800-85786400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:85780800-85786400	Weak transcription	Right Ventricle	heart
26	chr1:85780800-85787600	Weak transcription	Fetal Muscle Leg	muscle
27	chr1:85781000-85785600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:85781000-85785800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:85781800-85786000	Weak transcription	Placenta	Placenta
30	chr1:85781800-85786400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:85781800-85792800	Weak transcription	Pancreas	Pancrea
32	chr1:85782200-85790600	Genic enhancers	Muscle Satellite Cultured Cells	--
33	chr1:85782400-85785800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr1:85782400-85795000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:85782600-85785200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:85782800-85785600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr1:85782800-85785800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:85782800-85786400	Weak transcription	Lung	lung
39	chr1:85782800-85794600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr1:85783000-85795800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr1:85783200-85786200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:85783200-85786200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:85783200-85786400	Weak transcription	Fetal Intestine Small	intestine
44	chr1:85783200-85795800	Weak transcription	Aorta	Aorta
45	chr1:85783400-85785400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:85783600-85786200	Weak transcription	HSMMtube	muscle
47	chr1:85783800-85785600	Weak transcription	Fetal Kidney	kidney
48	chr1:85783800-85786000	Enhancers	A549	lung
49	chr1:85783800-85786200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:85783800-85789800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links