Variant report

Variant	rs12617529
Chromosome Location	chr2:47258528-47258529
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr2:47258361-47262673	SK-N-SH	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47257326..47259699-chr2:47417975..47420606,2	MCF-7	breast:
2	chr2:47258480..47260174-chr2:47263659..47266616,2	K562	blood:
3	chr2:47252454..47254562-chr2:47258233..47260100,2	K562	blood:
4	chr2:47257664..47259808-chr2:47380368..47382770,2	MCF-7	breast:
5	chr2:47252113..47260352-chr2:47399089..47405669,11	MCF-7	breast:
6	chr2:47246848..47250170-chr2:47255935..47259327,3	MCF-7	breast:
7	chr2:47252232..47263251-chr2:47397787..47406051,20	MCF-7	breast:

No data

Variant related genes	Relation type
TTC7A	TF binding region
ENSG00000239605	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11695952	0.87[MEX][hapmap];0.81[MKK][hapmap];0.82[AMR][1000 genomes]
rs1865257	0.80[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2304289	0.82[JPT][hapmap]
rs4952863	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4953445	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4953447	0.82[JPT][hapmap]
rs6717063	0.82[JPT][hapmap]
rs734269	0.82[EUR][1000 genomes]
rs7602479	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs892378	0.80[CEU][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs892379	0.80[CEU][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv525197	chr2:47210747-47297973	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv518312	chr2:47224927-47262137	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv984532	chr2:47237908-47270533	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv581752	chr2:47248111-47262137	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv525855	chr2:47249239-47259467	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv457363	chr2:47249239-47263232	Transcr. at gene 5' and 3' Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv581753	chr2:47249239-47263232	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv528091	chr2:47249239-47273732	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12617529	LOC100129726	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47214000-47262000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:47222000-47260600	Weak transcription	Small Intestine	intestine
3	chr2:47230200-47302800	Strong transcription	Dnd41	blood
4	chr2:47232000-47265000	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr2:47234400-47283600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:47236000-47278600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:47236600-47259200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:47236600-47259200	Weak transcription	Fetal Kidney	kidney
9	chr2:47237000-47260400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:47243800-47260200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:47243800-47260400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:47243800-47260800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:47243800-47261000	Weak transcription	K562	blood
14	chr2:47244000-47258800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:47244000-47260600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr2:47244200-47261200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:47244600-47258800	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr2:47244800-47258800	Strong transcription	Placenta	Placenta
19	chr2:47245800-47268600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:47246000-47260400	Strong transcription	Primary B cells from cord blood	blood
21	chr2:47246000-47260800	Strong transcription	Primary B cells from peripheral blood	blood
22	chr2:47246000-47260800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:47246000-47261800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr2:47246000-47283800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr2:47246200-47261400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:47246800-47281600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:47247000-47259800	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:47247400-47263000	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr2:47249000-47258800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:47249000-47259600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
31	chr2:47249200-47259200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:47249200-47259200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:47251600-47265000	Strong transcription	Primary T cells from cord blood	blood
34	chr2:47251600-47266000	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr2:47252000-47283400	Strong transcription	Thymus	Thymus
36	chr2:47252600-47260800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:47253400-47261400	Strong transcription	GM12878-XiMat	blood
38	chr2:47253400-47263000	Genic enhancers	Esophagus	oesophagus
39	chr2:47253600-47258800	Strong transcription	HSMM	muscle
40	chr2:47253800-47259800	Genic enhancers	HepG2	liver
41	chr2:47254000-47258800	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr2:47254400-47259400	Genic enhancers	Lung	lung
43	chr2:47254800-47258600	Weak transcription	Liver	Liver
44	chr2:47254800-47259000	Strong transcription	Fetal Intestine Large	intestine
45	chr2:47254800-47259200	Strong transcription	Fetal Intestine Small	intestine
46	chr2:47255200-47259000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:47255400-47259600	Weak transcription	Fetal Brain Male	brain
48	chr2:47255600-47258600	Strong transcription	Brain Substantia Nigra	brain
49	chr2:47255600-47258800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:47255600-47259000	Strong transcription	Colonic Mucosa	Colon

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