Variant report

Variant	rs6668200
Chromosome Location	chr1:179121280-179121281
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179108694..179110499-chr1:179120494..179123045,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10157885	0.89[EUR][1000 genomes]
rs10913690	0.89[YRI][hapmap]
rs12080991	1.00[CEU][hapmap]
rs13306729	0.81[CEU][hapmap]
rs17277358	1.00[CEU][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes]
rs17361990	1.00[CEU][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs17362128	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1856968	0.83[LWK][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs2017688	0.97[EUR][1000 genomes]
rs2066279	0.91[YRI][hapmap]
rs2130576	0.89[YRI][hapmap]
rs2274230	1.00[CEU][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes]
rs2636276	0.85[YRI][hapmap]
rs2636280	0.96[YRI][hapmap]
rs2791940	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs2791941	0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs2793793	0.80[AFR][1000 genomes]
rs2793796	0.83[LWK][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs2793798	0.89[YRI][hapmap]
rs2793803	0.92[YRI][hapmap]
rs2793812	0.83[LWK][hapmap];1.00[YRI][hapmap]
rs2816183	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs2816185	0.85[AFR][1000 genomes]
rs2816187	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs2816198	1.00[YRI][hapmap]
rs2816199	1.00[YRI][hapmap]
rs2816203	0.92[YRI][hapmap]
rs2816213	0.84[YRI][hapmap]
rs2816214	0.92[YRI][hapmap]
rs28459842	0.86[EUR][1000 genomes]
rs28914474	0.89[EUR][1000 genomes]
rs28914485	0.93[EUR][1000 genomes]
rs3753532	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs3813643	0.85[YRI][hapmap]
rs55642919	0.93[EUR][1000 genomes]
rs55825882	0.97[EUR][1000 genomes]
rs55827544	0.86[EUR][1000 genomes]
rs55920203	0.97[EUR][1000 genomes]
rs55955319	0.86[EUR][1000 genomes]
rs56382583	0.93[EUR][1000 genomes]
rs9650997	1.00[CEU][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes]
rs9650998	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9724754	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs9803885	0.83[EUR][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

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179099600-179122600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:179110200-179121400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:179111400-179121400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:179111400-179121400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:179112200-179121800	Weak transcription	Adipose Nuclei	Adipose
6	chr1:179112200-179121800	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:179112200-179124600	Weak transcription	Left Ventricle	heart
8	chr1:179112400-179121400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:179112400-179121400	Weak transcription	Small Intestine	intestine
10	chr1:179112400-179121600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:179112400-179133000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:179112400-179139000	Weak transcription	K562	blood
13	chr1:179113200-179133000	Weak transcription	Hela-S3	cervix
14	chr1:179113600-179121600	Weak transcription	Ovary	ovary
15	chr1:179116000-179121600	Weak transcription	Fetal Heart	heart
16	chr1:179116200-179121400	Weak transcription	HSMM	muscle
17	chr1:179116200-179122600	Weak transcription	NHLF	lung
18	chr1:179116200-179124000	Weak transcription	Osteobl	bone
19	chr1:179116200-179124400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:179116200-179133000	Weak transcription	NHDF-Ad	bronchial
21	chr1:179116400-179121400	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:179116400-179121400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:179116400-179133400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:179116600-179123400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:179116800-179122400	Weak transcription	HUVEC	blood vessel
26	chr1:179117800-179121400	Weak transcription	Thymus	Thymus
27	chr1:179117800-179133000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:179117800-179186000	Weak transcription	Fetal Stomach	stomach
29	chr1:179119000-179122600	Weak transcription	NH-A	brain
30	chr1:179119000-179135200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr1:179119400-179121600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:179119600-179121400	Enhancers	HepG2	liver
33	chr1:179119600-179133000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:179119800-179121400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:179119800-179123800	Enhancers	Liver	Liver
36	chr1:179120000-179122800	Enhancers	Fetal Intestine Large	intestine
37	chr1:179120200-179122000	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr1:179120200-179133800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:179120600-179121600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:179120800-179122000	Enhancers	Primary B cells from cord blood	blood
41	chr1:179121000-179122000	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr1:179121000-179122000	Enhancers	Stomach Mucosa	stomach
43	chr1:179121000-179122000	Flanking Active TSS	A549	lung
44	chr1:179121000-179122000	Enhancers	GM12878-XiMat	blood
45	chr1:179121000-179122400	Enhancers	Primary T cells from cord blood	blood
46	chr1:179121000-179122600	Enhancers	Primary B cells from peripheral blood	blood
47	chr1:179121000-179122600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr1:179121000-179125200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:179121200-179121600	Enhancers	Fetal Kidney	kidney
50	chr1:179121200-179121600	Active TSS	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links