Variant report

Variant	rs2636277
Chromosome Location	chr1:179122725-179122726
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179108694..179110499-chr1:179120494..179123045,2	MCF-7	breast:
2	chr1:179122193..179124932-chr1:179127076..179128871,2	K562	blood:
3	chr1:179121378..179123693-chr1:179125913..179128576,2	K562	blood:

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1078872	0.95[CHB][hapmap];1.00[CHD][hapmap]
rs10913690	0.95[CHB][hapmap];1.00[CHD][hapmap]
rs10913692	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10913693	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10913697	0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs12130276	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs1325195	1.00[CHB][hapmap]
rs1763022	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1826183	0.82[EUR][1000 genomes]
rs1856968	0.82[CHB][hapmap];0.98[CHD][hapmap];0.82[ASN][1000 genomes]
rs1858551	0.82[ASN][1000 genomes]
rs2066279	0.95[CHB][hapmap]
rs2087559	0.84[ASN][1000 genomes]
rs2130576	0.91[CHB][hapmap];1.00[CHD][hapmap]
rs2171958	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2171959	0.95[CHB][hapmap];1.00[CHD][hapmap];0.80[ASN][1000 genomes]
rs2258221	0.81[ASN][1000 genomes]
rs2306941	0.85[EUR][1000 genomes]
rs2486995	0.82[ASN][1000 genomes]
rs2486997	0.80[ASN][1000 genomes]
rs2486998	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2487563	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2493123	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2493124	0.95[CHB][hapmap];1.00[CHD][hapmap];0.80[ASN][1000 genomes]
rs2636274	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs2636275	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2636276	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs2636278	0.85[GIH][hapmap]
rs2636280	0.95[CHB][hapmap];1.00[CHD][hapmap]
rs2636291	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2636293	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs2791936	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2791940	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs2791941	0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs2791943	0.83[ASN][1000 genomes]
rs2791944	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2791945	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2793790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2793793	0.84[ASN][1000 genomes]
rs2793794	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2793796	0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs2793797	0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs2793798	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs2793800	0.81[EUR][1000 genomes]
rs2793801	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2793802	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2793803	0.95[CHB][hapmap]
rs2793810	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2793812	0.95[CHB][hapmap];1.00[CHD][hapmap]
rs2793813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2793816	0.95[CHB][hapmap];0.93[CHD][hapmap]
rs2816166	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2816168	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2816183	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs2816184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2816185	0.85[ASN][1000 genomes]
rs2816186	0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2816187	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs2816189	0.83[ASN][1000 genomes]
rs2816190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs2816191	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2816193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs2816198	0.95[CHB][hapmap]
rs2816199	0.95[CHB][hapmap]
rs2816200	0.82[EUR][1000 genomes]
rs2816201	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2816203	0.95[CHB][hapmap];1.00[CHD][hapmap]
rs2816207	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2816212	0.87[EUR][1000 genomes]
rs2816213	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs2816214	0.91[CHB][hapmap]
rs2816218	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3121198	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3122376	0.81[EUR][1000 genomes]
rs3813642	0.95[CHB][hapmap];1.00[CHD][hapmap]
rs3813643	0.95[CHB][hapmap];1.00[CHD][hapmap]
rs3829794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs411266	0.95[CHB][hapmap]
rs413613	0.88[EUR][1000 genomes]
rs451088	0.95[CHB][hapmap];0.98[CHD][hapmap]
rs4651013	0.95[CHB][hapmap]
rs915337	0.95[CHB][hapmap];1.00[CHD][hapmap]
rs9286921	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9425839	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs965401	0.84[ASN][1000 genomes]
rs9662858	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9726961	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs9727252	0.82[ASN][1000 genomes]
rs9728480	0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[ASN][1000 genomes]
rs9729129	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv1011462	chr1:179117101-179128290	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv1011210	chr1:179117101-179128676	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2636277	FAM20B	cis	parietal	SCAN
rs2636277	CACYBP	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179112200-179124600	Weak transcription	Left Ventricle	heart
2	chr1:179112400-179133000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:179112400-179139000	Weak transcription	K562	blood
4	chr1:179113200-179133000	Weak transcription	Hela-S3	cervix
5	chr1:179116200-179124000	Weak transcription	Osteobl	bone
6	chr1:179116200-179124400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:179116200-179133000	Weak transcription	NHDF-Ad	bronchial
8	chr1:179116400-179133400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:179116600-179123400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:179117800-179133000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:179117800-179186000	Weak transcription	Fetal Stomach	stomach
12	chr1:179119000-179135200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:179119600-179133000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:179119800-179123800	Enhancers	Liver	Liver
15	chr1:179120000-179122800	Enhancers	Fetal Intestine Large	intestine
16	chr1:179120200-179133800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:179121000-179125200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:179121200-179123000	Enhancers	Fetal Intestine Small	intestine
19	chr1:179121200-179123000	Enhancers	Psoas Muscle	Psoas
20	chr1:179121200-179136200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:179121400-179122800	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr1:179121400-179122800	Enhancers	Pancreas	Pancrea
23	chr1:179121400-179123000	Enhancers	Muscle Satellite Cultured Cells	--
24	chr1:179121400-179123000	Enhancers	HSMM	muscle
25	chr1:179121400-179123800	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr1:179121600-179125200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:179121600-179125800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:179121800-179122800	Enhancers	Adipose Nuclei	Adipose
29	chr1:179121800-179123400	Enhancers	Colon Smooth Muscle	Colon
30	chr1:179121800-179124200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:179121800-179126000	Enhancers	HepG2	liver
32	chr1:179121800-179135800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr1:179121800-179138400	Weak transcription	Aorta	Aorta
34	chr1:179122000-179123200	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr1:179122000-179123400	Enhancers	A549	lung
36	chr1:179122000-179124600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:179122000-179135000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr1:179122000-179139000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:179122000-179189400	Weak transcription	Primary B cells from cord blood	blood
40	chr1:179122200-179122800	Enhancers	Ovary	ovary
41	chr1:179122400-179122800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:179122400-179122800	Enhancers	Fetal Lung	lung
43	chr1:179122400-179122800	Enhancers	Right Atrium	heart
44	chr1:179122400-179123800	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr1:179122400-179153000	Weak transcription	Primary T cells from cord blood	blood
46	chr1:179122600-179122800	Enhancers	Lung	lung
47	chr1:179122600-179122800	Enhancers	Stomach Smooth Muscle	stomach
48	chr1:179122600-179122800	Enhancers	NH-A	brain
49	chr1:179122600-179122800	Enhancers	NHLF	lung
50	chr1:179122600-179123800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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