Variant report

Variant	rs13383563
Chromosome Location	chr2:152143524-152143525
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152140110..152142929-chr2:152143341..152145563,3	MCF-7	breast:
2	chr2:152142404..152144724-chr2:152266453..152268489,2	K562	blood:
3	chr2:152143066..152145503-chr2:152272183..152273824,2	MCF-7	breast:
4	chr2:152124835..152127070-chr2:152140941..152143645,2	K562	blood:
5	chr2:152115426..152120009-chr2:152142898..152146726,5	K562	blood:
6	chr2:152143136..152144934-chr2:152266709..152268489,3	K562	blood:

Variant related genes	Relation type
ENSG00000184898	Chromatin interaction
ENSG00000080345	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10207595	0.93[EUR][1000 genomes]
rs11694240	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12622615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs172341	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs2113509	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2161841	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28638170	0.80[EUR][1000 genomes]
rs289830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289831	1.00[CEU][hapmap];0.94[GIH][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs289834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs289836	0.97[EUR][1000 genomes]
rs289837	0.81[EUR][1000 genomes]
rs289838	0.81[CEU][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs289839	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs289840	0.85[EUR][1000 genomes]
rs289882	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs289883	0.93[CEU][hapmap];0.97[GIH][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes]
rs289887	0.93[EUR][1000 genomes]
rs289916	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs394884	0.81[EUR][1000 genomes]
rs446791	0.81[GIH][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs453226	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4665120	0.81[CEU][hapmap];0.86[GIH][hapmap]
rs4665123	0.85[CEU][hapmap]
rs55946491	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60381734	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6725961	1.00[CEU][hapmap];0.88[GIH][hapmap];0.81[TSI][hapmap]
rs6734376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744450	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523849	chr2:151718133-152143524	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS 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 target site	21 gene(s)	inside rSNPs	diseases
2	esv3693426	chr2:151725792-152295862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv834417	chr2:151980473-152154950	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1012891	chr2:152019809-152306897	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats 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 miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv1012139	chr2:152114637-152389516	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv1011339	chr2:152114637-152392940	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv999748	chr2:152135514-152476396	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
10	esv1793984	chr2:152138749-152154163	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152118800-152144000	Weak transcription	Stomach Mucosa	stomach
2	chr2:152118800-152144200	Weak transcription	Psoas Muscle	Psoas
3	chr2:152119000-152145000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:152119000-152145200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:152119000-152145200	Weak transcription	NHEK	skin
6	chr2:152119000-152145800	Weak transcription	HSMM	muscle
7	chr2:152119400-152144400	Weak transcription	A549	lung
8	chr2:152119400-152144800	Weak transcription	Brain Substantia Nigra	brain
9	chr2:152119400-152145200	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:152121200-152145000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:152121200-152145400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:152125200-152145400	Weak transcription	Aorta	Aorta
13	chr2:152125800-152145200	Weak transcription	Right Ventricle	heart
14	chr2:152126800-152145200	Weak transcription	HMEC	breast
15	chr2:152126800-152145600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:152127000-152145400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr2:152128000-152144600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr2:152128400-152145200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:152128600-152145200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:152130200-152145600	Weak transcription	Fetal Kidney	kidney
21	chr2:152130600-152144600	Weak transcription	Fetal Lung	lung
22	chr2:152134400-152144800	Weak transcription	Esophagus	oesophagus
23	chr2:152134400-152145200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:152134400-152145400	Weak transcription	Gastric	stomach
25	chr2:152134800-152144800	Weak transcription	Fetal Stomach	stomach
26	chr2:152134800-152144800	Weak transcription	Pancreas	Pancrea
27	chr2:152134800-152144800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:152134800-152145000	Weak transcription	Colonic Mucosa	Colon
29	chr2:152135000-152144600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:152135000-152144800	Weak transcription	Lung	lung
31	chr2:152135000-152145200	Weak transcription	NHLF	lung
32	chr2:152135200-152144800	Weak transcription	Left Ventricle	heart
33	chr2:152135400-152144800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:152135400-152145200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:152136600-152145200	Weak transcription	NH-A	brain
36	chr2:152136800-152144200	Weak transcription	HUVEC	blood vessel
37	chr2:152137200-152145400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:152137400-152144800	Weak transcription	Osteobl	bone
39	chr2:152137400-152145200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:152138600-152144200	Weak transcription	Hela-S3	cervix
41	chr2:152139000-152144600	Weak transcription	Brain Anterior Caudate	brain
42	chr2:152139200-152144000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:152139200-152144000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr2:152139200-152144000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:152139200-152144200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:152139200-152144200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:152139200-152144200	Weak transcription	Adipose Nuclei	Adipose
48	chr2:152139200-152144200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr2:152139200-152144400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:152139200-152144600	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links