Variant report

Variant	rs2396574
Chromosome Location	chr7:112475522-112475523
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10249952	1.00[CHB][hapmap]
rs10273589	0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs10275208	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs11762737	0.83[CHD][hapmap]
rs11768787	0.82[CHD][hapmap]
rs1227163	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1227171	0.84[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs1227174	0.81[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs1227181	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1227190	0.81[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs1238698	0.85[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs12535487	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs12539085	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap]
rs1530756	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs1533851	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1547554	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17160078	1.00[CHB][hapmap]
rs1718944	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718948	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1718961	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1718967	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17405723	0.83[CHD][hapmap]
rs1796492	0.81[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs1796493	0.81[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs1796512	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1796516	0.81[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs1996843	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2396573	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2457	0.81[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs2687267	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708295	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2708296	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3997335	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3997336	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs494324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs548994	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs549688	0.82[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs552304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs564494	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs565641	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58858661	0.92[EUR][1000 genomes]
rs62472532	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6466421	0.82[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs660743	0.95[CEU][hapmap];0.85[JPT][hapmap]
rs672911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs685259	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6944843	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs6948575	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6953522	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6967716	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs726593	0.82[JPT][hapmap]
rs7777973	0.95[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]
rs7781871	1.00[CHB][hapmap]
rs7785774	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803405	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7806781	0.82[CHB][hapmap]
rs7808616	1.00[CHB][hapmap]
rs821782	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821783	1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs821785	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs821787	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9969347	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.95[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	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	esv2752144	chr7:112398372-112499924	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers 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 target site	7 gene(s)	inside rSNPs	diseases
3	esv1794529	chr7:112400060-112588376	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1031405	chr7:112431403-112476756	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv429801	chr7:112434049-112477049	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
6	esv2752145	chr7:112434049-112500049	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
7	nsv1023222	chr7:112434413-112476756	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
8	nsv1034863	chr7:112434413-112504160	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
9	nsv5905	chr7:112445425-112521797	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2396574	CAV2	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112460800-112486000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:112466600-112476200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:112468000-112476000	Weak transcription	Gastric	stomach
4	chr7:112468600-112479200	Weak transcription	Fetal Brain Male	brain
5	chr7:112468600-112550000	Weak transcription	Aorta	Aorta
6	chr7:112469800-112529000	Weak transcription	Brain Anterior Caudate	brain
7	chr7:112470000-112478000	Weak transcription	Psoas Muscle	Psoas
8	chr7:112470200-112479000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr7:112470200-112479400	Weak transcription	Small Intestine	intestine
10	chr7:112470200-112480000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr7:112470400-112478000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr7:112470600-112482800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr7:112470600-112485800	Weak transcription	Fetal Heart	heart
14	chr7:112470800-112479600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr7:112470800-112483200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr7:112470800-112490200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr7:112470800-112493000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr7:112470800-112498000	Weak transcription	Fetal Kidney	kidney
19	chr7:112470800-112502800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr7:112470800-112506800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr7:112470800-112533200	Weak transcription	HSMM	muscle
22	chr7:112471000-112477200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr7:112471000-112482000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr7:112471000-112482800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr7:112471200-112482600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr7:112471800-112475800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr7:112471800-112476000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr7:112471800-112479600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr7:112471800-112479800	Weak transcription	Adipose Nuclei	Adipose
30	chr7:112471800-112495400	Weak transcription	Left Ventricle	heart
31	chr7:112471800-112502000	Weak transcription	Fetal Stomach	stomach
32	chr7:112471800-112511200	Weak transcription	HSMMtube	muscle
33	chr7:112471800-112545200	Weak transcription	Ovary	ovary
34	chr7:112472000-112475800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr7:112472000-112477600	Weak transcription	Brain Germinal Matrix	brain
36	chr7:112472000-112479800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr7:112472000-112487800	Weak transcription	Fetal Intestine Large	intestine
38	chr7:112472000-112491600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr7:112472000-112492200	Weak transcription	Fetal Lung	lung
40	chr7:112472000-112497800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr7:112472000-112506400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr7:112472000-112524600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr7:112472200-112475600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr7:112472200-112477800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr7:112472200-112487600	Weak transcription	Fetal Intestine Small	intestine
46	chr7:112472200-112493400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr7:112472200-112513200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr7:112472200-112517800	Weak transcription	Osteobl	bone
49	chr7:112472400-112489200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr7:112472600-112475600	Weak transcription	Primary B cells from cord blood	blood

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