Variant report

Variant	rs2180442
Chromosome Location	chr20:16330934-16330935
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs12624939	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12625552	1.00[CHB][hapmap]
rs12625709	0.81[ASN][1000 genomes]
rs1590872	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1884603	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1884604	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1884605	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1884606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2093004	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2144883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2144885	1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs2144886	1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes]
rs2144887	1.00[JPT][hapmap]
rs2144889	1.00[JPT][hapmap]
rs2144890	1.00[JPT][hapmap]
rs2144891	1.00[JPT][hapmap]
rs2180443	1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes]
rs2208057	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2208058	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2208059	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2328016	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2328017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2328018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2328019	1.00[CEU][hapmap];0.88[GIH][hapmap];0.96[LWK][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2328020	1.00[JPT][hapmap]
rs4814469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4814477	0.81[AMR][1000 genomes]
rs4814478	1.00[JPT][hapmap]
rs6034438	1.00[CHB][hapmap]
rs6034439	1.00[CHB][hapmap]
rs6034446	1.00[CHB][hapmap]
rs6034447	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs6034453	0.81[ASN][1000 genomes]
rs6034460	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6034461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6034464	1.00[JPT][hapmap]
rs6034466	0.81[TSI][hapmap]
rs6034487	1.00[CHB][hapmap]
rs6043852	1.00[CHB][hapmap]
rs6043854	1.00[CHB][hapmap]
rs6043858	1.00[CHB][hapmap]
rs6043870	1.00[CHB][hapmap]
rs6043879	1.00[CHB][hapmap]
rs6043881	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6043882	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6043887	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6043892	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6043904	0.91[GIH][hapmap]
rs6043911	1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes]
rs6043913	1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs6075048	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6075051	1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs6080229	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6080243	1.00[JPT][hapmap]
rs6080244	1.00[JPT][hapmap]
rs6105582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105603	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6111060	0.88[GIH][hapmap]
rs6111075	1.00[JPT][hapmap]
rs6111076	1.00[JPT][hapmap]
rs6135739	1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes]
rs7268027	1.00[JPT][hapmap]
rs7271622	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8117949	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8119246	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8122535	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs913826	0.95[CEU][hapmap];0.85[GIH][hapmap];0.81[TSI][hapmap];0.87[EUR][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	nsv833931	chr20:16308276-16460596	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16262600-16346200	Weak transcription	Gastric	stomach
2	chr20:16276400-16348200	Weak transcription	Colon Smooth Muscle	Colon
3	chr20:16288000-16332400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr20:16289400-16348000	Weak transcription	Colonic Mucosa	Colon
5	chr20:16291400-16331000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr20:16295600-16349000	Weak transcription	HepG2	liver
7	chr20:16296600-16345200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr20:16298800-16333400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr20:16312400-16331200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr20:16315400-16331000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr20:16315400-16345000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr20:16315400-16346200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr20:16315400-16348000	Weak transcription	Fetal Intestine Large	intestine
14	chr20:16315400-16364400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr20:16315600-16331000	Weak transcription	Aorta	Aorta
16	chr20:16315600-16346200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr20:16315600-16348000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr20:16315600-16348400	Weak transcription	Spleen	Spleen
19	chr20:16315800-16357600	Weak transcription	Right Ventricle	heart
20	chr20:16316000-16332000	Weak transcription	Brain Anterior Caudate	brain
21	chr20:16316000-16344000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr20:16316000-16346200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr20:16316000-16384400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr20:16316200-16347200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr20:16318600-16346200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr20:16318600-16348400	Weak transcription	Esophagus	oesophagus
27	chr20:16318800-16345000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr20:16318800-16368200	Weak transcription	Primary B cells from cord blood	blood
29	chr20:16319000-16345800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr20:16319000-16346200	Weak transcription	Pancreas	Pancrea
31	chr20:16319000-16346400	Weak transcription	Fetal Intestine Small	intestine
32	chr20:16320600-16336600	Weak transcription	Primary T cells from cord blood	blood
33	chr20:16322600-16346000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr20:16326200-16346000	Weak transcription	Liver	Liver
35	chr20:16327000-16332800	Weak transcription	Fetal Stomach	stomach
36	chr20:16327200-16336600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr20:16327200-16336800	Weak transcription	Ovary	ovary
38	chr20:16327200-16344000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr20:16327400-16336000	Weak transcription	Adipose Nuclei	Adipose
40	chr20:16327400-16346400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr20:16327600-16348200	Weak transcription	Left Ventricle	heart
42	chr20:16329000-16331200	Enhancers	Psoas Muscle	Psoas
43	chr20:16329200-16345200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr20:16329400-16333400	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr20:16329600-16333000	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr20:16329800-16333600	Enhancers	Fetal Muscle Leg	muscle
47	chr20:16330000-16331400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr20:16330000-16332000	Enhancers	NHDF-Ad	bronchial
49	chr20:16330000-16332200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr20:16330000-16344800	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links