Variant report

Variant	rs12602494
Chromosome Location	chr17:46037607-46037608
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46037386..46040340-chr17:46123583..46126115,2	MCF-7	breast:
2	chr17:46035894..46038484-chr17:46099628..46103418,4	MCF-7	breast:
3	chr17:46033549..46039001-chr17:46046732..46050276,6	K562	blood:
4	chr17:46031321..46037809-chr17:46043555..46050276,13	K562	blood:
5	chr17:45907437..45910086-chr17:46037370..46039885,2	MCF-7	breast:
6	chr17:45969751..45975935-chr17:46032072..46038613,14	MCF-7	breast:
7	chr17:46009429..46012200-chr17:46035247..46037959,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108465	Chromatin interaction
ENSG00000266601	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000141294	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000159111	Chromatin interaction
ENSG00000264920	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11079801	0.85[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs11079803	0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs1108833	0.84[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs1130932	0.85[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs11545723	0.83[CHB][hapmap]
rs11652185	0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs11652827	0.85[ASN][1000 genomes]
rs11654010	0.83[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11655068	0.87[ASN][1000 genomes]
rs11655352	0.87[ASN][1000 genomes]
rs11659126	0.85[ASN][1000 genomes]
rs12601827	0.87[ASN][1000 genomes]
rs12939739	0.85[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs13353189	0.80[JPT][hapmap]
rs17617250	0.83[CHB][hapmap]
rs2228251	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2228253	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2229358	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2318118	0.85[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2325749	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2325751	0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs2525107	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2905851	0.81[CHB][hapmap]
rs3096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34593510	0.85[ASN][1000 genomes]
rs35280206	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36124074	0.85[ASN][1000 genomes]
rs3764396	0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs4369725	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4793731	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4793732	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4793733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4793734	0.83[CHB][hapmap]
rs4793737	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4794332	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6503934	0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs67194241	0.85[ASN][1000 genomes]
rs7208707	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs7211859	0.83[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs757351	0.83[CHB][hapmap]
rs8066893	0.83[ASN][1000 genomes]
rs8071003	0.85[ASN][1000 genomes]
rs9894188	0.82[ASN][1000 genomes]
rs9895863	0.85[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs9903223	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12602494	SCRN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
2	chr17:46027200-46047200	Weak transcription	Spleen	Spleen
3	chr17:46027600-46047400	Weak transcription	Right Ventricle	heart
4	chr17:46027600-46047600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr17:46028000-46047400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr17:46028000-46047600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:46030200-46045800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr17:46031400-46039000	Weak transcription	Primary T cells from cord blood	blood
9	chr17:46032000-46037800	Active TSS	Rectal Smooth Muscle	rectum
10	chr17:46032800-46037800	Enhancers	Fetal Thymus	thymus
11	chr17:46035000-46047400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr17:46035200-46038600	Weak transcription	Small Intestine	intestine
13	chr17:46035400-46038000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
14	chr17:46035600-46038000	Enhancers	Esophagus	oesophagus
15	chr17:46035800-46037800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr17:46035800-46037800	Weak transcription	NHEK	skin
17	chr17:46036000-46047200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr17:46036200-46043400	Weak transcription	A549	lung
19	chr17:46036400-46039200	Enhancers	Pancreas	Pancrea
20	chr17:46036600-46037800	Flanking Active TSS	Fetal Intestine Small	intestine
21	chr17:46036600-46047800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr17:46036800-46038400	Enhancers	HepG2	liver
23	chr17:46036800-46047400	Weak transcription	Thymus	Thymus
24	chr17:46037000-46038000	Enhancers	Colonic Mucosa	Colon
25	chr17:46037000-46038400	Weak transcription	Gastric	stomach
26	chr17:46037000-46038600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr17:46037200-46037800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
28	chr17:46037200-46037800	Flanking Active TSS	Fetal Intestine Large	intestine
29	chr17:46037200-46038000	Enhancers	Placenta Amnion	Placenta Amnion
30	chr17:46037200-46038000	Flanking Active TSS	Stomach Mucosa	stomach
31	chr17:46037600-46037800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr17:46037600-46037800	Active TSS	Duodenum Mucosa	Duodenum
33	chr17:46037600-46037800	Enhancers	Placenta	Placenta
34	chr17:46037600-46038000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr17:46037600-46038000	Enhancers	Fetal Heart	heart
36	chr17:46037600-46038000	Enhancers	K562	blood
37	chr17:46037600-46038200	Active TSS	Rectal Mucosa Donor 29	rectum

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