Variant report

Variant	rs12464428
Chromosome Location	chr2:20420716-20420717
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20301244..20303124-chr2:20419816..20421979,2	MCF-7	breast:
2	chr17:57152201..57154948-chr2:20418855..20421470,2	MCF-7	breast:
3	chr2:20414820..20416839-chr2:20419190..20421088,3	K562	blood:
4	chr2:20418331..20420755-chr21:46948637..46950137,2	MCF-7	breast:
5	chr2:20157887..20159473-chr2:20420201..20422160,2	MCF-7	breast:
6	chr2:20418255..20420764-chr20:52271543..52273696,2	MCF-7	breast:
7	chr2:20249888..20254017-chr2:20419396..20423263,3	MCF-7	breast:
8	chr2:20329860..20331531-chr2:20418864..20420895,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000223734	Chromatin interaction
ENSG00000068697	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1043400	0.82[CEU][hapmap]
rs10495704	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1106111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11096648	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11096649	0.94[ASN][1000 genomes]
rs11096650	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11888357	0.83[CEU][hapmap]
rs11895228	0.83[CEU][hapmap]
rs12373772	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12373819	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13415389	0.90[ASN][1000 genomes]
rs2002090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007340	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2348703	0.80[CEU][hapmap]
rs3732162	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs3732163	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732164	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755300	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3771227	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3771229	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771232	0.84[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs3771233	0.85[CEU][hapmap];0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs3771236	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3771238	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3771239	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3771240	0.84[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs3771241	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3771243	0.90[ASN][1000 genomes]
rs3771244	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3771246	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3771247	0.81[CEU][hapmap];0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs3796066	0.80[CEU][hapmap]
rs3821218	0.87[CEU][hapmap]
rs3821219	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57938873	0.90[ASN][1000 genomes]
rs59129757	0.90[ASN][1000 genomes]
rs62109740	0.90[ASN][1000 genomes]
rs62111433	0.90[ASN][1000 genomes]
rs6748274	0.83[CEU][hapmap]
rs72785203	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785204	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785206	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585590	0.93[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846803	chr2:20409322-20427189	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20391800-20423200	Weak transcription	Right Atrium	heart
2	chr2:20404000-20422400	Weak transcription	Brain Germinal Matrix	brain
3	chr2:20404600-20420800	Enhancers	Stomach Mucosa	stomach
4	chr2:20413200-20423000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:20413400-20421000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:20414000-20421400	Weak transcription	Hela-S3	cervix
7	chr2:20414200-20423000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:20414600-20421000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:20414600-20421600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:20414800-20421600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:20415000-20420800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:20415000-20421000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:20415200-20422000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:20415600-20422200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr2:20415800-20423200	Weak transcription	Small Intestine	intestine
16	chr2:20416000-20423800	Transcr. at gene 5' and 3'	NHEK	skin
17	chr2:20416200-20423200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:20417000-20420800	Enhancers	GM12878-XiMat	blood
19	chr2:20417200-20422000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr2:20417800-20422800	Transcr. at gene 5' and 3'	HMEC	breast
21	chr2:20418000-20422000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:20418200-20421000	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr2:20418400-20422400	Genic enhancers	HepG2	liver
24	chr2:20418600-20421000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr2:20418600-20421600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:20418600-20422000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr2:20418600-20422600	Weak transcription	Fetal Kidney	kidney
28	chr2:20418800-20421000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:20418800-20421800	Weak transcription	Fetal Brain Male	brain
30	chr2:20418800-20423000	Flanking Active TSS	Liver	Liver
31	chr2:20419000-20421400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:20419200-20422600	Enhancers	Fetal Intestine Large	intestine
33	chr2:20419400-20420800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr2:20419400-20422600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:20419600-20420800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:20420000-20420800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:20420000-20422000	Weak transcription	Colonic Mucosa	Colon
38	chr2:20420000-20422600	Genic enhancers	Fetal Intestine Small	intestine
39	chr2:20420200-20421000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr2:20420200-20422200	Weak transcription	Fetal Stomach	stomach
41	chr2:20420200-20422400	Weak transcription	Pancreas	Pancrea
42	chr2:20420200-20422400	Weak transcription	Spleen	Spleen
43	chr2:20420200-20422800	Weak transcription	Gastric	stomach
44	chr2:20420200-20422800	Enhancers	Placenta Amnion	Placenta Amnion
45	chr2:20420400-20420800	Transcr. at gene 5' and 3'	Placenta	Placenta
46	chr2:20420400-20420800	Weak transcription	Lung	lung
47	chr2:20420400-20421200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:20420400-20422000	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr2:20420400-20423200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:20420600-20420800	Genic enhancers	HUES48 Cell Line	embryonic stem cell

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