Variant report

Variant	rs13244634
Chromosome Location	chr7:5273464-5273465
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:5272109..5273708-chr7:5323100..5324631,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11520824	0.85[ASN][1000 genomes]
rs12472	0.89[CEU][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12534949	0.83[ASN][1000 genomes]
rs3807586	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4518565	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[ASN][1000 genomes]
rs58612269	0.85[ASN][1000 genomes]
rs62441068	0.87[ASN][1000 genomes]
rs62441951	0.81[ASN][1000 genomes]
rs62441953	0.83[ASN][1000 genomes]
rs62441954	0.83[ASN][1000 genomes]
rs9639939	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530968	chr7:4572250-5418004	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
3	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
4	nsv916396	chr7:5128917-5370805	Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer 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
5	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
6	nsv887390	chr7:5224407-5411296	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv887391	chr7:5224407-5572132	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	292 gene(s)	inside rSNPs	diseases
8	nsv830889	chr7:5248157-5427465	Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv8034	chr7:5257953-5417973	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
10	nsv887392	chr7:5263194-5359680	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13244634	WIPI2	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5231400-5279800	Weak transcription	Fetal Brain Male	brain
2	chr7:5234000-5274800	Weak transcription	Stomach Mucosa	stomach
3	chr7:5249000-5273600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:5249000-5273600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr7:5249200-5273600	Strong transcription	Fetal Intestine Small	intestine
6	chr7:5249800-5273600	Strong transcription	Fetal Brain Female	brain
7	chr7:5254200-5280000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr7:5254600-5273600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr7:5258000-5279600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr7:5266600-5276200	Weak transcription	Fetal Kidney	kidney
11	chr7:5267400-5279800	Weak transcription	Right Atrium	heart
12	chr7:5268200-5280000	Weak transcription	Psoas Muscle	Psoas
13	chr7:5269800-5274800	Weak transcription	K562	blood
14	chr7:5270200-5277000	Weak transcription	HSMMtube	muscle
15	chr7:5270200-5279800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr7:5271000-5276800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr7:5271000-5276800	Weak transcription	NHDF-Ad	bronchial
18	chr7:5271000-5279800	Weak transcription	A549	lung
19	chr7:5271000-5279800	Weak transcription	HMEC	breast
20	chr7:5271200-5274600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr7:5271200-5277800	Weak transcription	HepG2	liver
22	chr7:5271200-5279600	Weak transcription	NH-A	brain
23	chr7:5271200-5280000	Weak transcription	Colonic Mucosa	Colon
24	chr7:5271400-5279600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr7:5271400-5279800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr7:5271400-5280000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr7:5271600-5280000	Weak transcription	HUVEC	blood vessel
28	chr7:5271800-5275200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr7:5271800-5279800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr7:5272000-5275800	Enhancers	Primary B cells from cord blood	blood
31	chr7:5272000-5278600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr7:5272000-5279600	Weak transcription	Hela-S3	cervix
33	chr7:5272200-5273600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr7:5272200-5277000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr7:5272200-5277200	Weak transcription	Ovary	ovary
36	chr7:5272400-5277000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr7:5272400-5277600	Enhancers	Primary B cells from peripheral blood	blood
38	chr7:5272400-5279600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr7:5272400-5279600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr7:5272400-5279600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr7:5272400-5279600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr7:5272400-5279600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr7:5272400-5279800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr7:5272600-5273600	Genic enhancers	GM12878-XiMat	blood
45	chr7:5272600-5274000	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr7:5272600-5274600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr7:5272600-5275600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr7:5272600-5276800	Weak transcription	HSMM	muscle
49	chr7:5272600-5276800	Weak transcription	Osteobl	bone
50	chr7:5272600-5278200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links