Variant report

Variant	rs9879992
Chromosome Location	chr3:119712721-119712722
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	chr3:119712509..119715289-chr3:119716837..119718695,2	MCF-7	breast:

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10511395	0.90[CEU][hapmap]
rs1054191	0.90[CEU][hapmap]
rs10934500	0.82[YRI][hapmap]
rs10934503	0.84[YRI][hapmap]
rs10934506	0.85[YRI][hapmap]
rs10934507	0.82[YRI][hapmap]
rs1154596	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs1154597	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs11915717	0.85[YRI][hapmap]
rs11921053	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11929668	0.90[CEU][hapmap]
rs12494560	0.88[AMR][1000 genomes]
rs13312998	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs13314595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1579031	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16830683	1.00[CHB][hapmap]
rs16830689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1719887	1.00[CHB][hapmap]
rs1719888	1.00[CHB][hapmap]
rs1719889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1719895	1.00[CHB][hapmap]
rs1732170	0.82[CEU][hapmap]
rs182839	1.00[CHB][hapmap]
rs2037547	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs2461816	0.82[CHB][hapmap]
rs2461827	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2472680	0.82[CHB][hapmap]
rs28516957	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108749	1.00[CHB][hapmap]
rs334533	0.82[CEU][hapmap]
rs334534	1.00[CHB][hapmap]
rs334535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs334536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes]
rs334559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs334560	0.96[EUR][1000 genomes]
rs334561	1.00[CHB][hapmap]
rs334566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes]
rs3853592	0.84[ASN][1000 genomes]
rs4072520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4340737	0.85[YRI][hapmap]
rs4450859	0.95[AMR][1000 genomes]
rs4624596	0.85[YRI][hapmap]
rs4688042	0.85[YRI][hapmap]
rs4688043	1.00[CHB][hapmap]
rs4688046	0.85[YRI][hapmap]
rs4688047	0.85[YRI][hapmap]
rs4688054	0.85[YRI][hapmap]
rs56126162	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58043853	0.91[EUR][1000 genomes]
rs60272712	0.84[ASN][1000 genomes]
rs6438550	1.00[CHB][hapmap]
rs6438554	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs6438555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes]
rs66650215	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6762640	0.84[ASN][1000 genomes]
rs6769435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6774693	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6775397	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6779828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6784239	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs6785050	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs6790751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs6795874	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797689	1.00[CHB][hapmap]
rs6802301	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6805251	0.81[CEU][hapmap]
rs6807868	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs7613197	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7620750	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7624540	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7635604	0.84[ASN][1000 genomes]
rs7636600	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7644234	0.82[CEU][hapmap]
rs7649661	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7650554	1.00[CHB][hapmap]
rs7652172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9289138	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes]
rs9784393	1.00[CHB][hapmap]
rs9829763	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9851174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9859778	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119631000-119717000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:119656600-119718400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:119665800-119716800	Weak transcription	HSMM	muscle
4	chr3:119681200-119723200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:119687200-119716600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:119689000-119722600	Weak transcription	Gastric	stomach
7	chr3:119692400-119717000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:119692400-119723200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:119693600-119732200	Weak transcription	A549	lung
10	chr3:119700600-119722800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:119700800-119717000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:119701000-119720000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:119701000-119722600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:119701800-119717200	Weak transcription	Fetal Thymus	thymus
15	chr3:119706000-119717000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:119706200-119717000	Weak transcription	Primary B cells from cord blood	blood
17	chr3:119707400-119716600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:119708200-119716800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:119709000-119722600	Weak transcription	Ovary	ovary
20	chr3:119709200-119723000	Weak transcription	Spleen	Spleen
21	chr3:119709400-119716800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr3:119709600-119717000	Weak transcription	Left Ventricle	heart
23	chr3:119710200-119716400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:119710200-119716600	Weak transcription	HMEC	breast
25	chr3:119710200-119716800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:119710200-119716800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:119710200-119719000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:119710200-119722600	Weak transcription	Stomach Mucosa	stomach
29	chr3:119710200-119730800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:119710400-119716400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr3:119710400-119717000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:119710400-119717200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:119710400-119722800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr3:119710600-119712800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr3:119710800-119712800	Enhancers	Duodenum Mucosa	Duodenum
36	chr3:119711000-119717000	Weak transcription	Dnd41	blood
37	chr3:119711200-119712800	Enhancers	Liver	Liver
38	chr3:119711400-119719200	Weak transcription	NHEK	skin
39	chr3:119711400-119729200	Weak transcription	Colon Smooth Muscle	Colon
40	chr3:119711600-119716800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:119711800-119712800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:119711800-119712800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:119711800-119712800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:119711800-119712800	Enhancers	Adipose Nuclei	Adipose
45	chr3:119711800-119722800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr3:119711800-119723200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr3:119712000-119712800	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr3:119712000-119713000	Enhancers	Small Intestine	intestine
49	chr3:119712000-119713400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:119712000-119716800	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links