Variant report

Variant	rs6445259
Chromosome Location	chr3:52167173-52167174
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52165461..52167461-chr3:52184184..52186326,2	K562	blood:
2	chr3:52164710..52167219-chr3:52168743..52171613,3	K562	blood:
3	chr3:52162996..52167625-chr3:52168207..52172862,5	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10212560	1.00[MEX][hapmap]
rs11130297	1.00[EUR][1000 genomes]
rs1587921	1.00[EUR][1000 genomes]
rs17052020	1.00[EUR][1000 genomes]
rs56990501	1.00[EUR][1000 genomes]
rs5743838	1.00[EUR][1000 genomes]
rs60643756	1.00[EUR][1000 genomes]
rs6775662	1.00[EUR][1000 genomes]
rs6782809	1.00[EUR][1000 genomes]
rs6784563	0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs6784653	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6797786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7611413	1.00[ASW][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs7614535	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7617023	1.00[EUR][1000 genomes]
rs7623076	1.00[EUR][1000 genomes]
rs7625515	1.00[EUR][1000 genomes]
rs7636412	1.00[EUR][1000 genomes]
rs7652969	0.83[AMR][1000 genomes]
rs7652984	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs973948	1.00[EUR][1000 genomes]
rs973949	1.00[EUR][1000 genomes]
rs9813468	1.00[MEX][hapmap]
rs9834363	1.00[MEX][hapmap]
rs9836166	1.00[MEX][hapmap]
rs9845752	1.00[MEX][hapmap]
rs9860132	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
5	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52110600-52179400	Weak transcription	Brain Germinal Matrix	brain
2	chr3:52136800-52187200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:52140400-52178200	Strong transcription	Dnd41	blood
4	chr3:52148600-52179800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:52155200-52180000	Weak transcription	Fetal Intestine Large	intestine
6	chr3:52155200-52187200	Weak transcription	Colonic Mucosa	Colon
7	chr3:52156200-52178000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:52156200-52187600	Weak transcription	Primary T cells from cord blood	blood
9	chr3:52156600-52177800	Weak transcription	Fetal Brain Female	brain
10	chr3:52157200-52171600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:52157200-52187600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:52157400-52178200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:52157400-52187200	Weak transcription	Fetal Kidney	kidney
14	chr3:52157600-52178600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:52157800-52170200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:52158600-52172000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:52159800-52169200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:52160200-52170200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:52160200-52179600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:52160400-52167200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:52160600-52182600	Weak transcription	NHDF-Ad	bronchial
22	chr3:52160800-52169600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:52161200-52176400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:52161400-52169200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:52161400-52178000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:52162400-52167800	Weak transcription	Fetal Thymus	thymus
27	chr3:52162400-52184800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:52162600-52167400	Weak transcription	Gastric	stomach
29	chr3:52162600-52167400	Weak transcription	NHLF	lung
30	chr3:52162600-52167600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr3:52162600-52168800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr3:52162600-52170200	Weak transcription	Spleen	Spleen
33	chr3:52162600-52170600	Weak transcription	Osteobl	bone
34	chr3:52162600-52171400	Weak transcription	Right Ventricle	heart
35	chr3:52162600-52172600	Weak transcription	Ovary	ovary
36	chr3:52162800-52169000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:52162800-52169200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr3:52162800-52170200	Weak transcription	Brain Hippocampus Middle	brain
39	chr3:52162800-52170200	Weak transcription	Right Atrium	heart
40	chr3:52162800-52170200	Weak transcription	HUVEC	blood vessel
41	chr3:52162800-52170600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:52162800-52173200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:52162800-52173400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:52162800-52176400	Weak transcription	Placenta	Placenta
45	chr3:52162800-52176400	Weak transcription	HMEC	breast
46	chr3:52162800-52179400	Weak transcription	A549	lung
47	chr3:52162800-52187000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr3:52162800-52187200	Weak transcription	NH-A	brain
49	chr3:52163000-52167600	Weak transcription	Hela-S3	cervix
50	chr3:52163000-52176600	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links