Variant report

Variant	rs2013675
Chromosome Location	chr12:12605378-12605379
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12603843..12606415-chr12:12711459..12714793,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DUSP16-3	chr12:12605037-12605415	NONHSAT026970

Variant related genes	Relation type
ENSG00000111266	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10772567	1.00[YRI][hapmap]
rs10845544	1.00[YRI][hapmap]
rs11054901	1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs11829597	0.82[TSI][hapmap]
rs16907998	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs17312055	1.00[ASN][1000 genomes]
rs4570678	1.00[ASN][1000 genomes]
rs55946646	1.00[ASN][1000 genomes]
rs56188411	1.00[ASN][1000 genomes]
rs56325045	1.00[ASN][1000 genomes]
rs56340010	1.00[ASN][1000 genomes]
rs58809132	1.00[ASN][1000 genomes]
rs61913515	0.89[AMR][1000 genomes]
rs61913534	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61923612	1.00[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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv898810	chr12:12600080-12627410	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	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
rs2013675	GPR19	cis	lymphoblastoid	seeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12589800-12607200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:12590600-12614600	Weak transcription	Primary B cells from cord blood	blood
3	chr12:12594400-12618200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr12:12595200-12609200	Weak transcription	GM12878-XiMat	blood
5	chr12:12595200-12618600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:12596000-12620200	Weak transcription	HSMM	muscle
7	chr12:12596000-12629800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:12596200-12620600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:12596800-12618200	Weak transcription	Primary T cells from cord blood	blood
10	chr12:12596800-12618200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr12:12597000-12617800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:12597400-12618200	Weak transcription	Gastric	stomach
13	chr12:12597400-12629000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:12598000-12607200	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:12599000-12618600	Weak transcription	Left Ventricle	heart
16	chr12:12599600-12608600	Weak transcription	NHEK	skin
17	chr12:12600400-12609000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:12600600-12616800	Weak transcription	Fetal Stomach	stomach
19	chr12:12600800-12609000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:12600800-12610200	Weak transcription	Brain Anterior Caudate	brain
21	chr12:12601000-12607200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr12:12601000-12609000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr12:12601000-12620200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr12:12602200-12610600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:12602600-12610600	Weak transcription	Brain Angular Gyrus	brain
26	chr12:12602800-12605600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:12602800-12605600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:12602800-12610000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr12:12603200-12606600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:12603200-12609200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr12:12603200-12609400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:12603200-12609600	Weak transcription	Brain Substantia Nigra	brain
33	chr12:12603200-12618400	Weak transcription	Esophagus	oesophagus
34	chr12:12603400-12605600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr12:12603400-12618600	Weak transcription	Pancreas	Pancrea
36	chr12:12603800-12607200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:12603800-12614200	Weak transcription	Aorta	Aorta
38	chr12:12603800-12639200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr12:12604000-12609400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:12604000-12628600	Weak transcription	Fetal Lung	lung
41	chr12:12604400-12607200	Weak transcription	HepG2	liver
42	chr12:12604600-12608000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr12:12604600-12609800	Weak transcription	Hela-S3	cervix
44	chr12:12604600-12613600	Weak transcription	Fetal Intestine Small	intestine
45	chr12:12604600-12618600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:12605000-12605400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:12605200-12605400	Enhancers	Fetal Intestine Large	intestine
48	chr12:12605200-12618400	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links