Variant report

Variant	rs6078575
Chromosome Location	chr20:1295722-1295723
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	chr20:1293745..1297831-chr20:1304825..1308186,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125775	Chromatin interaction
ENSG00000234684	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11697322	1.00[CHB][hapmap]
rs11699494	1.00[CHB][hapmap]
rs13163	1.00[CHB][hapmap]
rs16994239	1.00[CHB][hapmap]
rs16994549	1.00[CHB][hapmap]
rs17793560	1.00[CHB][hapmap]
rs1883933	1.00[CHB][hapmap]
rs1884390	1.00[CHB][hapmap]
rs2064645	1.00[CHB][hapmap]
rs2064646	1.00[CHB][hapmap]
rs2873522	1.00[CHB][hapmap]
rs4577347	1.00[CHB][hapmap]
rs4813115	1.00[CHB][hapmap]
rs4814102	1.00[CHB][hapmap]
rs6033534	1.00[CHB][hapmap]
rs6033554	1.00[CHB][hapmap]
rs6033660	1.00[CHB][hapmap]
rs6033871	1.00[CHB][hapmap]
rs6033896	1.00[CHB][hapmap]
rs6033914	1.00[CHB][hapmap]
rs6033935	1.00[CHB][hapmap]
rs6041689	1.00[CHB][hapmap]
rs6041716	1.00[CHB][hapmap]
rs6041717	1.00[CHB][hapmap]
rs6042506	1.00[CHB][hapmap]
rs6042550	1.00[CHB][hapmap]
rs6042568	1.00[CHB][hapmap]
rs6042574	1.00[CHB][hapmap]
rs6042578	1.00[CHB][hapmap]
rs6042585	1.00[CHB][hapmap]
rs6042588	1.00[CHB][hapmap]
rs6042676	1.00[CHB][hapmap]
rs6042689	1.00[CHB][hapmap]
rs6105031	1.00[CHB][hapmap]
rs6105101	1.00[CHB][hapmap]
rs6109401	0.86[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109437	1.00[CHB][hapmap]
rs6109511	1.00[CHB][hapmap]
rs6109522	1.00[CHB][hapmap]
rs6109740	1.00[CHB][hapmap]
rs6109784	1.00[CHB][hapmap]
rs6109984	1.00[CHB][hapmap]
rs6109989	1.00[CHB][hapmap]
rs6110189	1.00[CHB][hapmap]
rs6110193	1.00[CHB][hapmap]
rs62187547	1.00[ASN][1000 genomes]
rs6514337	1.00[CHB][hapmap]
rs6514364	1.00[CHB][hapmap]
rs715217	1.00[CHB][hapmap]
rs747611	1.00[CHB][hapmap]
rs8117563	1.00[CHB][hapmap]
rs8118276	1.00[CHB][hapmap]
rs912113	1.00[CHB][hapmap]
rs958839	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057939	chr20:824980-1316778	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1057097	chr20:1030940-1314265	Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1067393	chr20:1254805-1302796	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv912588	chr20:1269588-1300456	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv912589	chr20:1272686-1298397	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv912590	chr20:1278770-1298397	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised 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
7	nsv912591	chr20:1283523-1296811	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Active 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	4 gene(s)	inside rSNPs	n/a
8	nsv912592	chr20:1283523-1297516	Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
9	nsv912593	chr20:1283523-1298397	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv912594	chr20:1283523-1299968	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv912595	chr20:1283523-1313762	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6078575	MRPL12	trans	cerebellum	SCAN
rs6078575	SLC4A11	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1282000-1298200	Weak transcription	A549	lung
2	chr20:1282200-1298600	Weak transcription	Thymus	Thymus
3	chr20:1283800-1301800	Weak transcription	HSMMtube	muscle
4	chr20:1284200-1303600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr20:1285200-1298200	Weak transcription	K562	blood
6	chr20:1287400-1298200	Weak transcription	Liver	Liver
7	chr20:1289600-1305000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr20:1293400-1302200	Weak transcription	Esophagus	oesophagus
9	chr20:1293800-1297400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr20:1293800-1298200	Weak transcription	Lung	lung
11	chr20:1294000-1299200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr20:1294200-1299600	Weak transcription	Fetal Intestine Large	intestine
13	chr20:1294200-1301600	Weak transcription	Spleen	Spleen
14	chr20:1294200-1302000	Weak transcription	Gastric	stomach
15	chr20:1294200-1302200	Weak transcription	Pancreas	Pancrea
16	chr20:1294200-1305600	Weak transcription	Ovary	ovary
17	chr20:1294400-1298200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr20:1294400-1300000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr20:1294400-1301600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr20:1294400-1304800	Weak transcription	Placenta	Placenta
21	chr20:1294600-1297600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr20:1294600-1297800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr20:1294600-1298000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr20:1294600-1298000	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr20:1294600-1298200	Weak transcription	NHLF	lung
26	chr20:1294600-1298400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr20:1294600-1298800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr20:1294600-1299600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr20:1294600-1302800	Weak transcription	NHEK	skin
30	chr20:1294600-1305200	Weak transcription	Colon Smooth Muscle	Colon
31	chr20:1294600-1305200	Weak transcription	Fetal Thymus	thymus
32	chr20:1294600-1305400	Weak transcription	Colonic Mucosa	Colon
33	chr20:1294800-1298000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr20:1294800-1298200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr20:1294800-1298200	Weak transcription	NHDF-Ad	bronchial
36	chr20:1294800-1298200	Weak transcription	Osteobl	bone
37	chr20:1294800-1298400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr20:1294800-1298400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr20:1294800-1302200	Weak transcription	Adipose Nuclei	Adipose
40	chr20:1294800-1305200	Weak transcription	Dnd41	blood
41	chr20:1295000-1296000	Weak transcription	Fetal Intestine Small	intestine
42	chr20:1295000-1297800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr20:1295000-1300800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr20:1295000-1302200	Weak transcription	Stomach Mucosa	stomach
45	chr20:1295000-1302200	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links