Variant report

Variant	rs7980390
Chromosome Location	chr12:12599949-12599950
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12598434..12601352-chr12:12712226..12715206,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111266	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11830917	1.00[CHD][hapmap]
rs11831188	1.00[ASN][1000 genomes]
rs11831555	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16908006	0.93[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[ASN][1000 genomes]
rs16908019	1.00[ASN][1000 genomes]
rs16908222	1.00[CHD][hapmap]
rs17312912	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1861674	0.86[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.89[MKK][hapmap];1.00[ASN][1000 genomes]
rs2193270	0.93[ASW][hapmap];0.83[GIH][hapmap];0.81[LWK][hapmap];0.82[MKK][hapmap]
rs3741797	1.00[CHD][hapmap]
rs4763288	1.00[JPT][hapmap]
rs4763289	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4763824	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763827	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4763828	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763831	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4763837	1.00[CHD][hapmap]
rs56261569	0.81[ASN][1000 genomes]
rs58218344	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58529509	1.00[ASN][1000 genomes]
rs60022096	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60363317	1.00[ASN][1000 genomes]
rs60971404	1.00[ASN][1000 genomes]
rs6488521	1.00[ASN][1000 genomes]
rs6488523	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488524	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488527	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133988	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7134787	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7135655	0.83[GIH][hapmap]
rs714480	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7306292	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7309982	0.83[GIH][hapmap]
rs73287587	1.00[ASN][1000 genomes]
rs7957014	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973069	1.00[ASN][1000 genomes]
rs7975061	1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7978842	1.00[ASN][1000 genomes]
rs888198	1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7980390	CLEC6A	cis	parietal	SCAN
rs7980390	LOH12CR1	cis	cerebellum	SCAN
rs7980390	EPS8	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12587400-12600200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:12587400-12600200	Weak transcription	Ovary	ovary
3	chr12:12589800-12607200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:12590400-12601800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:12590600-12614600	Weak transcription	Primary B cells from cord blood	blood
6	chr12:12592200-12600400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:12592200-12602200	Enhancers	Fetal Thymus	thymus
8	chr12:12594400-12600200	Weak transcription	Lung	lung
9	chr12:12594400-12618200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr12:12594800-12600400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:12595000-12602200	Weak transcription	Placenta	Placenta
12	chr12:12595200-12600200	Weak transcription	Fetal Intestine Large	intestine
13	chr12:12595200-12602800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr12:12595200-12609200	Weak transcription	GM12878-XiMat	blood
15	chr12:12595200-12618600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr12:12595800-12600200	Weak transcription	Fetal Intestine Small	intestine
17	chr12:12596000-12602200	Weak transcription	A549	lung
18	chr12:12596000-12620200	Weak transcription	HSMM	muscle
19	chr12:12596000-12629800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:12596200-12600000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:12596200-12620600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:12596400-12600600	Weak transcription	Hela-S3	cervix
23	chr12:12596400-12603200	Weak transcription	Aorta	Aorta
24	chr12:12596600-12601000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr12:12596800-12602000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr12:12596800-12602400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr12:12596800-12603000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr12:12596800-12604600	Weak transcription	NHLF	lung
29	chr12:12596800-12618200	Weak transcription	Primary T cells from cord blood	blood
30	chr12:12596800-12618200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:12597000-12600000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr12:12597000-12600200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr12:12597000-12600200	Weak transcription	Right Atrium	heart
34	chr12:12597000-12600400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr12:12597000-12601600	Weak transcription	Spleen	Spleen
36	chr12:12597000-12602400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:12597000-12602600	Weak transcription	Esophagus	oesophagus
38	chr12:12597000-12603000	Weak transcription	Psoas Muscle	Psoas
39	chr12:12597000-12617800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:12597200-12600000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:12597200-12600000	Weak transcription	Brain Hippocampus Middle	brain
42	chr12:12597200-12603000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr12:12597400-12600200	Weak transcription	Fetal Stomach	stomach
44	chr12:12597400-12601600	Weak transcription	Pancreas	Pancrea
45	chr12:12597400-12601800	Weak transcription	Liver	Liver
46	chr12:12597400-12618200	Weak transcription	Gastric	stomach
47	chr12:12597400-12629000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr12:12597600-12600200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:12597600-12600200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:12597600-12600200	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links