Variant report

Variant	rs3771233
Chromosome Location	chr2:20416048-20416049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20415298..20418162-chr2:20421703..20423542,3	K562	blood:
2	chr2:20414820..20416839-chr2:20419190..20421088,3	K562	blood:
3	chr2:20366147..20368368-chr2:20415586..20417297,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115884	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10175853	0.88[CEU][hapmap]
rs10192042	0.87[CEU][hapmap]
rs10495704	0.83[CEU][hapmap];0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs1106111	0.84[CEU][hapmap];0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs11096648	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11096649	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11096650	0.86[ASN][1000 genomes]
rs12373772	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12373819	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12464428	0.85[CEU][hapmap];0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs13415389	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2002090	0.84[CEU][hapmap];0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs2007340	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3732162	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3732163	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3732164	0.83[CEU][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3755300	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3771229	0.86[ASN][1000 genomes]
rs3771232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3771236	0.85[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3771238	0.84[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3771239	0.84[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3771240	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3771241	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3771243	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3771244	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3771246	0.87[ASN][1000 genomes]
rs3771247	0.96[CEU][hapmap];0.93[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3821219	0.86[ASN][1000 genomes]
rs57938873	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59129757	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62109740	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62111433	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72785203	0.86[ASN][1000 genomes]
rs72785204	0.86[ASN][1000 genomes]
rs72785206	0.86[ASN][1000 genomes]
rs7558833	0.87[CEU][hapmap]
rs7563245	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs7585590	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9306890	0.88[CEU][hapmap]

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	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	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:58 , 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	chr2:20405800-20416200	Enhancers	Gastric	stomach
5	chr2:20410400-20416200	Genic enhancers	Fetal Intestine Small	intestine
6	chr2:20410600-20417400	Enhancers	Fetal Intestine Large	intestine
7	chr2:20412600-20420600	Weak transcription	NHLF	lung
8	chr2:20412800-20416400	Enhancers	Rectal Mucosa Donor 29	rectum
9	chr2:20413000-20416200	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr2:20413000-20417600	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr2:20413200-20420600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:20413200-20423000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:20413400-20419800	Weak transcription	Pancreas	Pancrea
14	chr2:20413400-20420600	Weak transcription	NH-A	brain
15	chr2:20413400-20421000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:20413800-20417600	Enhancers	Duodenum Mucosa	Duodenum
17	chr2:20413800-20418400	Weak transcription	Fetal Lung	lung
18	chr2:20414000-20416600	Enhancers	GM12878-XiMat	blood
19	chr2:20414000-20417400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:20414000-20421400	Weak transcription	Hela-S3	cervix
21	chr2:20414200-20418200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:20414200-20418200	Weak transcription	Spleen	Spleen
23	chr2:20414200-20420200	Strong transcription	Fetal Stomach	stomach
24	chr2:20414200-20420400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:20414200-20423000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:20414600-20416200	Weak transcription	Fetal Thymus	thymus
27	chr2:20414600-20417000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr2:20414600-20421000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:20414600-20421600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:20414800-20416800	Genic enhancers	Esophagus	oesophagus
31	chr2:20414800-20417200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr2:20414800-20419400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:20414800-20419800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:20414800-20420200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr2:20414800-20420400	Genic enhancers	Placenta	Placenta
36	chr2:20414800-20420600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:20414800-20421600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:20415000-20418600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr2:20415000-20420800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr2:20415000-20421000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr2:20415200-20418600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:20415200-20422000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:20415400-20416400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr2:20415400-20417800	Enhancers	Colonic Mucosa	Colon
45	chr2:20415400-20418200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr2:20415400-20418200	Weak transcription	Fetal Kidney	kidney
47	chr2:20415400-20419600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:20415600-20416400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:20415600-20422200	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr2:20415800-20417600	Enhancers	Liver	Liver

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