Variant report

Variant	rs6802301
Chromosome Location	chr3:119753324-119753325
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11921053	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12494560	0.84[AMR][1000 genomes]
rs13314595	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1579031	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16830683	0.84[ASN][1000 genomes]
rs16830689	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1719889	0.92[AMR][1000 genomes]
rs182839	0.84[ASN][1000 genomes]
rs184576	0.82[ASN][1000 genomes]
rs28516957	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs334534	0.84[ASN][1000 genomes]
rs334535	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334536	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs334552	0.84[ASN][1000 genomes]
rs334554	0.84[ASN][1000 genomes]
rs334559	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334560	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs334561	0.81[ASN][1000 genomes]
rs334566	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4072520	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4450859	0.92[AMR][1000 genomes]
rs56126162	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58043853	0.92[EUR][1000 genomes]
rs6438555	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66650215	0.83[EUR][1000 genomes]
rs6769435	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6770314	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6771023	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6774693	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6775397	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6779828	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790751	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs6795874	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6797689	0.84[ASN][1000 genomes]
rs6805931	0.84[ASN][1000 genomes]
rs7613197	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7617372	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7620750	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7628426	0.84[ASN][1000 genomes]
rs7636600	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7649661	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7650554	0.84[ASN][1000 genomes]
rs7652172	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289138	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs968824	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9851174	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859778	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879992	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[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:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119732600-119757800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:119737400-119754000	Weak transcription	Small Intestine	intestine
3	chr3:119737800-119757200	Weak transcription	A549	lung
4	chr3:119739400-119756000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:119740000-119758200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:119740800-119753400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:119741000-119758000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:119741200-119758400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:119741800-119753600	Weak transcription	Thymus	Thymus
10	chr3:119742000-119754400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:119742000-119758000	Weak transcription	NHDF-Ad	bronchial
12	chr3:119742600-119757000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr3:119744200-119758000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:119744400-119758400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:119744800-119753600	Weak transcription	Fetal Thymus	thymus
16	chr3:119744800-119758000	Weak transcription	NHEK	skin
17	chr3:119745000-119757000	Weak transcription	Dnd41	blood
18	chr3:119745200-119758400	Weak transcription	HepG2	liver
19	chr3:119745400-119758400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:119747400-119756200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:119747600-119758400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:119747800-119757000	Weak transcription	Lung	lung
23	chr3:119747800-119757200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:119747800-119757200	Weak transcription	Ovary	ovary
25	chr3:119747800-119758400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:119748000-119758000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:119748400-119756400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:119748600-119755800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:119748800-119753600	Weak transcription	Left Ventricle	heart
30	chr3:119748800-119754600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:119748800-119756800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:119748800-119757800	Weak transcription	Right Ventricle	heart
33	chr3:119749000-119758400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:119749200-119753600	Weak transcription	Psoas Muscle	Psoas
35	chr3:119749400-119755200	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:119749600-119758000	Weak transcription	HSMM	muscle
37	chr3:119750000-119753400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr3:119750200-119757000	Weak transcription	Esophagus	oesophagus
39	chr3:119750400-119754600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr3:119750400-119758400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:119750600-119755200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:119750600-119757800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:119750600-119758000	Weak transcription	Fetal Lung	lung
44	chr3:119751600-119753400	ZNF genes & repeats	GM12878-XiMat	blood
45	chr3:119751800-119766800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:119752000-119753400	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr3:119752200-119757200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr3:119753000-119753600	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr3:119753000-119753600	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr3:119753000-119753800	Enhancers	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links