Variant report

Variant	rs2339509
Chromosome Location	chr10:52303980-52303981
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52303296..52304994-chr10:52312451..52315128,2	MCF-7	breast:
2	chr10:52303071..52304706-chr10:52310411..52312427,2	K562	blood:
3	chr10:52291845..52294288-chr10:52302987..52304879,2	K562	blood:
4	chr10:52291845..52294615-chr10:52303379..52304888,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs2208035	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2208037	0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339508	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2860490	0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983348	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2983352	0.93[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983358	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983362	0.81[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983363	0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983365	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983372	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3001855	0.81[YRI][hapmap]
rs3011708	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011711	0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011768	0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3011778	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011781	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011799	0.94[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094723	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription 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	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52280200-52328000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr10:52286400-52304000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr10:52296800-52306000	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr10:52297000-52304400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr10:52297000-52304600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr10:52297400-52306000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr10:52299000-52304000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr10:52299000-52304400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr10:52299000-52305400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr10:52299000-52305400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr10:52299000-52310200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr10:52299200-52304000	Weak transcription	Fetal Intestine Small	intestine
13	chr10:52299200-52304600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr10:52299200-52305800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr10:52299200-52310200	Weak transcription	Pancreas	Pancrea
16	chr10:52299600-52320600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr10:52300200-52305000	Weak transcription	HepG2	liver
18	chr10:52300600-52310200	Weak transcription	Placenta	Placenta
19	chr10:52300800-52304600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr10:52300800-52304800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr10:52300800-52310800	Weak transcription	Gastric	stomach
22	chr10:52300800-52322800	Weak transcription	Primary B cells from cord blood	blood
23	chr10:52301400-52304000	Weak transcription	Right Ventricle	heart
24	chr10:52301400-52304800	Weak transcription	Psoas Muscle	Psoas
25	chr10:52301400-52306000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr10:52301400-52308600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr10:52301600-52304200	Enhancers	Brain Anterior Caudate	brain
28	chr10:52301600-52304400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr10:52301600-52306000	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr10:52301600-52309200	Weak transcription	Ovary	ovary
31	chr10:52301600-52310200	Weak transcription	Left Ventricle	heart
32	chr10:52301600-52327200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr10:52301800-52304000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr10:52302400-52306000	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr10:52302600-52305000	Enhancers	Brain Substantia Nigra	brain
36	chr10:52302600-52305200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr10:52302600-52306000	Enhancers	Primary T cells from cord blood	blood
38	chr10:52302800-52304200	Genic enhancers	K562	blood
39	chr10:52302800-52304400	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr10:52302800-52304800	Enhancers	Small Intestine	intestine
41	chr10:52302800-52306000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr10:52303000-52304400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr10:52303000-52304400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr10:52303000-52304600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr10:52303000-52305000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr10:52303000-52305200	Enhancers	GM12878-XiMat	blood
47	chr10:52303200-52304000	Weak transcription	Brain Angular Gyrus	brain
48	chr10:52303200-52304200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr10:52303200-52310200	Weak transcription	Fetal Lung	lung
50	chr10:52303200-52310200	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links