Variant report

Variant	rs12500519
Chromosome Location	chr4:85756030-85756031
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10856852	0.83[TSI][hapmap]
rs11097026	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs11097028	0.89[EUR][1000 genomes]
rs12501525	0.94[ASN][1000 genomes]
rs12502294	0.82[EUR][1000 genomes]
rs12502409	0.87[EUR][1000 genomes]
rs12502559	0.85[EUR][1000 genomes]
rs12503330	0.84[EUR][1000 genomes]
rs12511112	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs13108722	0.81[EUR][1000 genomes]
rs13118671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13125323	0.86[EUR][1000 genomes]
rs13139541	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13141072	0.83[EUR][1000 genomes]
rs1484661	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1508670	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs16995920	0.82[EUR][1000 genomes]
rs17009317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17009334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17009341	0.80[CEU][hapmap];0.88[TSI][hapmap]
rs2046404	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs2218323	0.80[CHD][hapmap];0.91[JPT][hapmap]
rs2869216	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs3098928	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs35190829	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35892581	0.85[EUR][1000 genomes]
rs3747680	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs4383611	0.84[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs4533765	0.83[TSI][hapmap]
rs4590017	0.89[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs55871210	0.89[EUR][1000 genomes]
rs55912355	0.82[EUR][1000 genomes]
rs56094216	0.85[EUR][1000 genomes]
rs58074983	0.87[EUR][1000 genomes]
rs6531777	0.80[CEU][hapmap];0.88[TSI][hapmap]
rs6531782	0.83[TSI][hapmap]
rs6531783	0.89[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs66965560	0.82[EUR][1000 genomes]
rs67624868	0.87[EUR][1000 genomes]
rs6815917	0.87[EUR][1000 genomes]
rs6816534	0.83[EUR][1000 genomes]
rs6820517	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6825852	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs6829807	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6838727	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs6847067	0.90[JPT][hapmap]
rs6847564	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6858666	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs71631375	0.82[EUR][1000 genomes]
rs72664928	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72664957	0.91[EUR][1000 genomes]
rs7654035	0.80[CEU][hapmap]
rs7661609	0.80[CEU][hapmap];0.88[TSI][hapmap]
rs7663580	0.83[TSI][hapmap]
rs7682896	0.82[EUR][1000 genomes]
rs7685537	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs7690054	0.84[EUR][1000 genomes]
rs7692223	0.89[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs7694949	0.80[CEU][hapmap];0.88[TSI][hapmap]
rs7695054	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7699226	0.80[CEU][hapmap];0.90[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv532738	chr4:85590841-85777997	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv427684	chr4:85668487-85863446	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12500519	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85696400-85757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:85697400-85772800	Weak transcription	Small Intestine	intestine
3	chr4:85701600-85783000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:85705400-85770000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:85708600-85777400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr4:85709000-85769600	Weak transcription	Right Ventricle	heart
7	chr4:85709000-85781600	Weak transcription	Esophagus	oesophagus
8	chr4:85709200-85770200	Weak transcription	Psoas Muscle	Psoas
9	chr4:85722200-85787600	Weak transcription	Gastric	stomach
10	chr4:85722400-85762600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:85723000-85821000	Weak transcription	Pancreas	Pancrea
12	chr4:85723200-85770400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr4:85723200-85777000	Weak transcription	Colon Smooth Muscle	Colon
14	chr4:85724000-85781400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:85724000-85786600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:85724200-85761600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr4:85724200-85769600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr4:85727800-85783200	Weak transcription	Colonic Mucosa	Colon
19	chr4:85730800-85760400	Weak transcription	Fetal Kidney	kidney
20	chr4:85731400-85769600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:85731400-85791600	Weak transcription	Lung	lung
22	chr4:85731800-85769600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:85732800-85759000	Weak transcription	Brain Angular Gyrus	brain
24	chr4:85732800-85761200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr4:85735800-85777000	Weak transcription	Aorta	Aorta
26	chr4:85736400-85758800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:85736400-85769600	Weak transcription	A549	lung
28	chr4:85736400-85790600	Weak transcription	NHEK	skin
29	chr4:85738600-85761000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:85738800-85760400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:85739400-85777000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr4:85739800-85759000	Weak transcription	Brain Substantia Nigra	brain
33	chr4:85740400-85756400	Weak transcription	Brain Hippocampus Middle	brain
34	chr4:85741800-85756400	Weak transcription	Brain Germinal Matrix	brain
35	chr4:85742400-85757600	Weak transcription	Brain Anterior Caudate	brain
36	chr4:85742600-85757000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr4:85742600-85783200	Weak transcription	Fetal Brain Male	brain
38	chr4:85742800-85761600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr4:85742800-85769600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr4:85742800-85777000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr4:85743000-85759000	Weak transcription	Left Ventricle	heart
42	chr4:85745600-85759000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr4:85746400-85759400	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr4:85747200-85769600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr4:85747800-85768000	Weak transcription	HepG2	liver
46	chr4:85748000-85761200	Weak transcription	NHLF	lung
47	chr4:85749400-85769600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:85749600-85759000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:85750000-85760600	Weak transcription	Fetal Intestine Small	intestine
50	chr4:85750200-85761200	Weak transcription	Stomach Smooth Muscle	stomach

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