Variant report

Variant	rs7559305
Chromosome Location	chr2:20839725-20839726
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20633992..20655025-chr2:20829429..20854651,127	MCF-7	breast:
2	chr2:20834621..20842195-chr2:20845758..20852616,8	MCF-7	breast:
3	chr2:20835349..20838099-chr2:20838875..20841328,3	MCF-7	breast:
4	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:
5	chr2:20784510..20786983-chr2:20839378..20841496,2	MCF-7	breast:
6	chr2:20839547..20841831-chr2:20843514..20846128,3	K562	blood:
7	chr2:20837273..20840218-chr2:20850500..20852819,2	K562	blood:

Variant related genes	Relation type
ENSG00000228950	Chromatin interaction
ENSG00000269976	Chromatin interaction
ENSG00000118960	Chromatin interaction
ENSG00000143878	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1047176	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11676170	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11678019	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11688002	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs12470344	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13030108	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732149	0.90[CEU][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3732152	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3732154	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3732157	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3796065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3821217	0.95[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55788833	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56096206	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56174003	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56203116	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56240532	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56336286	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6531247	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6719474	0.94[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6721558	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs6723273	0.95[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6728166	0.95[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72782378	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72782380	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72782396	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72784306	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7586298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7609280	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs896733	0.95[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1008473	chr2:20811359-20879186	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv535599	chr2:20811359-20879186	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv517472	chr2:20814583-20855176	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv873725	chr2:20814583-20855176	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv527901	chr2:20818458-20876386	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
7	nsv999269	chr2:20824833-20869372	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
8	nsv873726	chr2:20829962-20876260	Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
9	nsv873727	chr2:20838318-20876260	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20815000-20847600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:20817400-20847600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr2:20817600-20850000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:20818800-20842400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:20819000-20847400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:20819400-20847800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr2:20820600-20849400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:20820800-20849600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:20823000-20842000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr2:20825400-20841000	Weak transcription	Primary B cells from cord blood	blood
11	chr2:20828600-20841800	Strong transcription	Primary T cells from cord blood	blood
12	chr2:20828800-20847800	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr2:20832600-20850000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:20833000-20841800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr2:20833800-20842000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:20833800-20843000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr2:20834400-20842000	Weak transcription	Fetal Thymus	thymus
18	chr2:20834800-20841000	Weak transcription	Hela-S3	cervix
19	chr2:20834800-20841800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:20834800-20849600	Weak transcription	Small Intestine	intestine
21	chr2:20835400-20841400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr2:20835400-20849800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr2:20835600-20840000	Weak transcription	Osteobl	bone
24	chr2:20835600-20840200	Weak transcription	Fetal Brain Female	brain
25	chr2:20835600-20840600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:20835600-20840600	Weak transcription	NH-A	brain
27	chr2:20835600-20840800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:20835600-20841200	Weak transcription	HSMM	muscle
29	chr2:20835600-20842000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:20835600-20847400	Weak transcription	HSMMtube	muscle
31	chr2:20835600-20847600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:20835600-20848800	Weak transcription	Fetal Lung	lung
33	chr2:20835600-20849600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:20835600-20849800	Weak transcription	Fetal Heart	heart
35	chr2:20835800-20840800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:20835800-20841000	Weak transcription	NHEK	skin
37	chr2:20835800-20843000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:20836000-20839800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr2:20836000-20840600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr2:20836000-20840800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:20836000-20841200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:20836000-20841400	Strong transcription	Lung	lung
43	chr2:20836000-20841600	Strong transcription	Spleen	Spleen
44	chr2:20836000-20841800	Strong transcription	Fetal Intestine Large	intestine
45	chr2:20836000-20841800	Strong transcription	Placenta	Placenta
46	chr2:20836000-20841800	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:20836000-20841800	Weak transcription	HMEC	breast
48	chr2:20836000-20842000	Strong transcription	Fetal Intestine Small	intestine
49	chr2:20836000-20847400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:20836000-20847600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links