Variant report

Variant	rs7569370
Chromosome Location	chr2:54216349-54216350
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54214773..54216416-chr2:54226494..54228805,2	MCF-7	breast:
2	chr2:54196870..54199646-chr2:54215437..54217712,2	MCF-7	breast:
3	chr2:54213667..54216386-chr2:54218063..54220465,2	K562	blood:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction
ENSG00000068878	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10084355	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10181999	0.80[EUR][1000 genomes]
rs10186566	0.81[EUR][1000 genomes]
rs10201364	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10203576	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10208233	0.81[EUR][1000 genomes]
rs1058320	0.92[CEU][hapmap]
rs1075265	0.92[CEU][hapmap]
rs11125519	0.83[EUR][1000 genomes]
rs11683654	0.93[CHB][hapmap];0.85[ASN][1000 genomes]
rs11687324	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11893270	0.80[EUR][1000 genomes]
rs12616212	0.91[EUR][1000 genomes]
rs12713253	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13414393	0.86[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.80[MEX][hapmap];0.87[ASN][1000 genomes]
rs1363062	1.00[CEU][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1363063	0.92[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1421617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1421622	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17268179	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2111868	0.91[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2112122	0.80[EUR][1000 genomes]
rs2287642	0.92[CEU][hapmap]
rs2884254	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2909460	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4671872	0.85[CEU][hapmap]
rs6545376	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545378	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6545380	0.83[EUR][1000 genomes]
rs6545384	0.83[AMR][1000 genomes]
rs6545388	0.85[CEU][hapmap]
rs6711105	0.80[EUR][1000 genomes]
rs6715488	0.84[EUR][1000 genomes]
rs6724389	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs6743455	0.80[EUR][1000 genomes]
rs6749817	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs698858	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs718872	0.92[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7566894	0.85[CEU][hapmap]
rs7569214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7571086	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7609017	0.87[EUR][1000 genomes]
rs805308	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805322	0.89[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes]
rs805341	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs805342	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs805343	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805345	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805359	0.82[AMR][1000 genomes]
rs805360	0.87[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap]
rs805366	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs805367	0.89[CEU][hapmap];0.93[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs805373	0.81[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap]
rs805374	0.81[CEU][hapmap];0.93[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs805375	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs805410	0.82[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs805412	0.93[CHB][hapmap];0.82[JPT][hapmap]
rs805423	0.85[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs805438	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs805439	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs805444	0.80[EUR][1000 genomes]
rs805450	0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs805453	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs918357	0.92[CEU][hapmap];0.82[TSI][hapmap]
rs929734	0.92[CEU][hapmap]
rs9631059	0.83[EUR][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	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7569370	C2orf73	cis	cerebellum	SCAN
rs7569370	ACYP2	cis	Muscle Skeletal	GTEx
rs7569370	ACYP2	cis	multi-tissue	Pritchard

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54199000-54221600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:54199000-54228800	Weak transcription	Aorta	Aorta
3	chr2:54200200-54216600	Weak transcription	Right Ventricle	heart
4	chr2:54200400-54218400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:54204400-54226400	Weak transcription	Pancreas	Pancrea
6	chr2:54205200-54222600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:54206000-54216600	Weak transcription	Esophagus	oesophagus
8	chr2:54206000-54221600	Weak transcription	Thymus	Thymus
9	chr2:54206000-54226400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr2:54206400-54220000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr2:54208200-54221400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:54208400-54248200	Weak transcription	Lung	lung
13	chr2:54208600-54216600	Weak transcription	Gastric	stomach
14	chr2:54208600-54219000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:54208600-54220200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:54208800-54216600	Weak transcription	Brain Angular Gyrus	brain
17	chr2:54209000-54221400	Weak transcription	Fetal Thymus	thymus
18	chr2:54209000-54221600	Weak transcription	Dnd41	blood
19	chr2:54211200-54216600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr2:54211200-54219000	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr2:54211200-54220600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr2:54211400-54217800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr2:54211400-54220200	Weak transcription	Primary B cells from cord blood	blood
24	chr2:54211400-54243000	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:54213600-54249800	Weak transcription	Left Ventricle	heart
26	chr2:54213800-54217200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr2:54214200-54217000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:54214800-54216600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:54214800-54217200	Weak transcription	Fetal Stomach	stomach
30	chr2:54214800-54219000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr2:54215000-54216400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:54215000-54216600	Weak transcription	Adipose Nuclei	Adipose
33	chr2:54215000-54216600	Weak transcription	Brain Anterior Caudate	brain
34	chr2:54215000-54216600	Weak transcription	Brain Substantia Nigra	brain
35	chr2:54215000-54216800	Weak transcription	Brain Hippocampus Middle	brain
36	chr2:54215000-54216800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr2:54215000-54219000	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:54215000-54219200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr2:54215000-54220600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:54215000-54226000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:54215000-54226000	Weak transcription	HSMMtube	muscle
42	chr2:54215000-54242800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:54215200-54216600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:54215200-54216600	Weak transcription	Primary T cells from cord blood	blood
45	chr2:54215200-54216600	Weak transcription	Liver	Liver
46	chr2:54215200-54216600	Weak transcription	Stomach Mucosa	stomach
47	chr2:54215200-54219200	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:54215200-54219400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:54215200-54220000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr2:54215200-54220000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links