Variant report

Variant	rs12519774
Chromosome Location	chr5:37703522-37703523
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:37702513..37704538-chr5:37716164..37718117,2	MCF-7	breast:
2	chr5:37667989..37670619-chr5:37702239..37705026,2	MCF-7	breast:
3	chr5:37702838..37705165-chr5:37705788..37708573,2	MCF-7	breast:
4	chr5:37664491..37667181-chr5:37703176..37705396,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10461983	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10941361	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11749343	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11749345	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12513493	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12517792	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12520294	0.88[ASN][1000 genomes]
rs12521092	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12651803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12656733	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs13154033	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13159969	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13171010	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13182520	0.87[ASN][1000 genomes]
rs13182737	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs13185923	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13187416	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1363925	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16903666	0.83[CHB][hapmap]
rs1862577	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1874178	0.83[CHB][hapmap]
rs2973086	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4431371	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];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4869542	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs525463	0.83[CHB][hapmap]
rs581376	0.83[CHB][hapmap]
rs665327	0.83[CHB][hapmap]
rs677084	0.83[CHB][hapmap];1.00[YRI][hapmap]
rs682825	0.83[CHB][hapmap]
rs6897494	0.91[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs7700431	0.83[CHB][hapmap]
rs781794	0.83[CHB][hapmap];1.00[YRI][hapmap]
rs870100	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs9292665	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.88[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	nsv1026554	chr5:37112133-37734859	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv537726	chr5:37112133-37734859	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv949716	chr5:37179341-37967352	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv1023871	chr5:37330018-37804744	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv537729	chr5:37330018-37804744	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv432744	chr5:37374124-37743077	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv597846	chr5:37430215-37813591	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1030250	chr5:37478163-37734859	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv881383	chr5:37485316-37773877	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12519774	RXFP3	cis	cerebellum	SCAN
rs12519774	SLC1A3	cis	parietal	SCAN
rs12519774	OXCT1	cis	parietal	SCAN
rs12519774	LIFR	cis	parietal	SCAN
rs12519774	GDNF	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37684400-37705000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:37685200-37743200	Weak transcription	Gastric	stomach
3	chr5:37685400-37717600	Weak transcription	Pancreas	Pancrea
4	chr5:37685600-37711200	Weak transcription	Fetal Stomach	stomach
5	chr5:37685600-37727000	Weak transcription	Lung	lung
6	chr5:37687200-37720600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr5:37688400-37721400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr5:37688400-37721400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr5:37688400-37723600	Weak transcription	Placenta	Placenta
10	chr5:37689600-37726000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr5:37692200-37721200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr5:37693800-37705200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr5:37695200-37716600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:37695400-37706000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr5:37695400-37715600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:37695400-37722600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr5:37695600-37706400	Weak transcription	Liver	Liver
18	chr5:37695600-37721200	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr5:37695800-37705200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr5:37696000-37717000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr5:37696200-37709800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr5:37696400-37717200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:37696600-37704600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr5:37696800-37710400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr5:37696800-37711200	Weak transcription	HSMMtube	muscle
26	chr5:37696800-37717000	Weak transcription	HSMM	muscle
27	chr5:37696800-37717400	Weak transcription	Small Intestine	intestine
28	chr5:37696800-37722800	Weak transcription	Psoas Muscle	Psoas
29	chr5:37697000-37705800	Weak transcription	Brain Anterior Caudate	brain
30	chr5:37697000-37706000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:37697000-37717000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr5:37697000-37721400	Weak transcription	Fetal Thymus	thymus
33	chr5:37697000-37743800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr5:37697200-37710400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:37697200-37710400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr5:37697200-37717000	Weak transcription	NH-A	brain
37	chr5:37697400-37705000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr5:37697400-37706000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr5:37697400-37710200	Weak transcription	NHDF-Ad	bronchial
40	chr5:37697400-37711000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr5:37697400-37717000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr5:37697400-37717200	Weak transcription	Hela-S3	cervix
43	chr5:37697400-37722200	Weak transcription	HMEC	breast
44	chr5:37698000-37705000	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr5:37698800-37716400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr5:37698800-37721000	Weak transcription	Dnd41	blood
47	chr5:37699000-37717400	Weak transcription	Ovary	ovary
48	chr5:37699200-37717000	Weak transcription	Fetal Intestine Large	intestine
49	chr5:37699200-37717600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:37699800-37717000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links