Variant report

Variant	rs2395880
Chromosome Location	chr7:107074264-107074265
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 147 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs10464499	0.88[ASN][1000 genomes]
rs10464620	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10487271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10953534	0.81[ASN][1000 genomes]
rs10953535	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10953536	0.89[EUR][1000 genomes]
rs10953537	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10953541	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs1121312	0.81[ASN][1000 genomes]
rs11532774	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11761181	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11764448	0.81[ASN][1000 genomes]
rs11766060	0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11766131	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769527	0.81[ASN][1000 genomes]
rs11769861	0.84[EUR][1000 genomes]
rs11769901	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11770061	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11773514	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12056231	0.86[ASN][1000 genomes]
rs12154285	0.85[EUR][1000 genomes]
rs12155231	0.82[EUR][1000 genomes]
rs12531187	0.85[EUR][1000 genomes]
rs12532447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12532514	0.89[EUR][1000 genomes]
rs12532849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs12532967	0.80[ASN][1000 genomes]
rs12533516	0.80[ASN][1000 genomes]
rs12533694	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12534000	0.82[EUR][1000 genomes]
rs12534124	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12534676	0.81[EUR][1000 genomes]
rs12535038	0.85[ASN][1000 genomes]
rs12535081	0.84[EUR][1000 genomes]
rs12535093	0.89[EUR][1000 genomes]
rs12535258	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12535761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12535814	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12536485	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12536491	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12536603	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12537011	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12537733	0.82[EUR][1000 genomes]
rs12537785	0.91[EUR][1000 genomes]
rs12538090	0.83[EUR][1000 genomes]
rs12538769	0.85[EUR][1000 genomes]
rs12538848	0.85[EUR][1000 genomes]
rs12539895	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13234124	0.82[ASN][1000 genomes]
rs1548523	0.81[EUR][1000 genomes]
rs1548524	0.81[EUR][1000 genomes]
rs17349904	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs17350182	0.81[ASN][1000 genomes]
rs17403088	0.81[CEU][hapmap];0.93[CHB][hapmap];0.90[ASN][1000 genomes]
rs17404067	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17428071	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs17428126	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17428504	0.81[ASN][1000 genomes]
rs17429118	0.82[EUR][1000 genomes]
rs17429146	0.82[EUR][1000 genomes]
rs17429825	0.91[EUR][1000 genomes]
rs17481621	0.90[ASN][1000 genomes]
rs17481842	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17482494	0.88[ASN][1000 genomes]
rs17482543	0.88[ASN][1000 genomes]
rs17486	0.90[ASN][1000 genomes]
rs1978085	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1989814	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2189501	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2249043	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];0.82[EUR][1000 genomes]
rs2283041	0.88[ASN][1000 genomes]
rs2299422	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2299428	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2395859	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2395881	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2894459	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34084719	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34523267	0.82[ASN][1000 genomes]
rs3757713	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3779497	0.93[ASN][1000 genomes]
rs3779498	0.81[ASN][1000 genomes]
rs3801958	0.82[EUR][1000 genomes]
rs3801959	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3801963	1.00[CEU][hapmap]
rs3815148	0.81[ASN][1000 genomes]
rs3823959	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3823960	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4515482	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4727683	0.81[ASN][1000 genomes]
rs4730228	0.80[ASN][1000 genomes]
rs4730229	0.81[ASN][1000 genomes]
rs4730231	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4730232	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4730233	0.85[EUR][1000 genomes]
rs4730239	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4730241	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4730242	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4730248	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4730250	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs5002976	0.91[EUR][1000 genomes]
rs56949084	0.85[ASN][1000 genomes]
rs57525841	0.81[ASN][1000 genomes]
rs58319984	0.82[EUR][1000 genomes]
rs58663672	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59782202	0.91[EUR][1000 genomes]
rs59900773	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60255281	0.81[EUR][1000 genomes]
rs61511581	0.81[EUR][1000 genomes]
rs6945784	0.85[ASN][1000 genomes]
rs6947674	0.86[ASN][1000 genomes]
rs6955488	0.88[ASN][1000 genomes]
rs6957186	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6958969	0.85[ASN][1000 genomes]
rs6960813	0.81[ASN][1000 genomes]
rs6963917	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6964395	0.96[ASN][1000 genomes]
rs6964798	0.80[ASN][1000 genomes]
rs6964966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6965001	0.80[ASN][1000 genomes]
rs6976759	0.88[ASN][1000 genomes]
rs6979198	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6979368	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs763386	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs7779062	0.80[ASN][1000 genomes]
rs7781947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7783181	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7783562	0.82[ASN][1000 genomes]
rs7784906	0.88[ASN][1000 genomes]
rs7785962	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7797791	0.85[ASN][1000 genomes]
rs7800443	0.81[ASN][1000 genomes]
rs7801317	0.88[ASN][1000 genomes]
rs7803290	0.80[ASN][1000 genomes]
rs7804979	0.89[EUR][1000 genomes]
rs7807154	0.88[ASN][1000 genomes]
rs7807648	0.82[EUR][1000 genomes]
rs7809508	0.89[EUR][1000 genomes]
rs7810216	0.89[EUR][1000 genomes]
rs8180747	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs997311	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3383027	chr7:106802625-107096474	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	esv1825788	chr7:106897237-107136320	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1024793	chr7:106900877-107170312	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv1832266	chr7:106961882-107136320	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
6	nsv1019963	chr7:107033342-107188641	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv539052	chr7:107033342-107188641	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2395880	LHFPL3	cis	parietal	SCAN
rs2395880	GPR22	Cis_1M	lymphoblastoid	RTeQTL
rs2395880	COG5	cis	parietal	SCAN
rs2395880	NRCAM	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107027800-107086800	Weak transcription	Aorta	Aorta
2	chr7:107028200-107082400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr7:107028200-107103800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr7:107035800-107133000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr7:107037800-107102200	Weak transcription	Ovary	ovary
6	chr7:107038800-107100600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr7:107046400-107081800	Weak transcription	HSMM	muscle
8	chr7:107046800-107082200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr7:107050600-107102400	Weak transcription	Dnd41	blood
10	chr7:107050800-107100200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr7:107051400-107087000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:107051600-107079000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:107051600-107082600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr7:107051800-107088600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr7:107052000-107098600	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr7:107052600-107126400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr7:107056800-107082400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:107065000-107100600	Weak transcription	Thymus	Thymus
19	chr7:107067600-107074400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:107067600-107119800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr7:107068200-107098400	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr7:107068400-107082400	Weak transcription	Left Ventricle	heart
23	chr7:107068400-107104000	Weak transcription	Pancreas	Pancrea
24	chr7:107069400-107086400	Weak transcription	Primary T cells from cord blood	blood
25	chr7:107072400-107076000	Weak transcription	Fetal Intestine Small	intestine
26	chr7:107072400-107100000	Weak transcription	Gastric	stomach
27	chr7:107072600-107082400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr7:107073000-107103600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr7:107074200-107081800	Weak transcription	Primary B cells from cord blood	blood

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