Variant report

Variant	rs12502409
Chromosome Location	chr4:85699579-85699580
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10856852	0.84[TSI][hapmap]
rs11097028	0.82[EUR][1000 genomes]
rs11725121	0.83[EUR][1000 genomes]
rs12500519	0.87[EUR][1000 genomes]
rs12502294	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12511112	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs13108722	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13118671	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs1484661	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1508670	0.95[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs16995920	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17009317	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs17009334	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs17009341	0.88[TSI][hapmap]
rs2218323	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs2869216	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs3098928	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs35190829	0.86[EUR][1000 genomes]
rs36036245	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3747680	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4590017	0.85[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap]
rs55871210	0.82[EUR][1000 genomes]
rs6531777	0.88[TSI][hapmap]
rs6815917	0.80[EUR][1000 genomes]
rs6816534	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6820517	0.82[EUR][1000 genomes]
rs6825852	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6829807	0.89[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6838727	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6847067	0.90[JPT][hapmap]
rs6847564	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6858666	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs72664928	0.88[EUR][1000 genomes]
rs72664957	0.84[EUR][1000 genomes]
rs7661609	0.88[TSI][hapmap]
rs7685537	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs7692223	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs7694949	0.88[TSI][hapmap]
rs7695054	0.87[EUR][1000 genomes]
rs7699226	0.88[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
rs12502409	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85619200-85726000	Weak transcription	Hela-S3	cervix
2	chr4:85636400-85701200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:85657000-85704200	Weak transcription	Psoas Muscle	Psoas
4	chr4:85664000-85703400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:85664000-85703600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:85664200-85703600	Weak transcription	Right Ventricle	heart
7	chr4:85668600-85703800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:85669600-85703600	Weak transcription	Aorta	Aorta
9	chr4:85670600-85700600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:85672200-85702400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:85672400-85700600	Weak transcription	Spleen	Spleen
12	chr4:85672400-85707000	Weak transcription	Colonic Mucosa	Colon
13	chr4:85672800-85700600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:85672800-85703600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:85672800-85703600	Weak transcription	Esophagus	oesophagus
16	chr4:85672800-85703600	Weak transcription	NHLF	lung
17	chr4:85673000-85700600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:85673200-85703600	Weak transcription	HepG2	liver
19	chr4:85673600-85700800	Weak transcription	Lung	lung
20	chr4:85673800-85700600	Weak transcription	Pancreas	Pancrea
21	chr4:85674600-85702200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:85675000-85700600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:85675200-85702800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:85675200-85703600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr4:85675600-85703600	Weak transcription	Fetal Brain Male	brain
26	chr4:85675800-85700400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr4:85676200-85700800	Weak transcription	HMEC	breast
28	chr4:85676600-85700600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:85677200-85707200	Weak transcription	NHEK	skin
30	chr4:85678400-85700600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:85678400-85700600	Weak transcription	Fetal Muscle Leg	muscle
32	chr4:85678400-85700600	Weak transcription	Gastric	stomach
33	chr4:85678400-85703600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:85679000-85700400	Weak transcription	Fetal Intestine Small	intestine
35	chr4:85683800-85732000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr4:85684800-85725000	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr4:85687200-85703000	Weak transcription	NH-A	brain
38	chr4:85688800-85725600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:85689400-85701400	Strong transcription	HSMM	muscle
40	chr4:85689600-85717200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr4:85689800-85700600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr4:85689800-85700600	Weak transcription	Left Ventricle	heart
43	chr4:85689800-85703600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr4:85690000-85722000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr4:85690800-85725600	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr4:85691000-85724800	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr4:85691600-85712200	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr4:85691600-85718400	Strong transcription	Placenta	Placenta
49	chr4:85691800-85703800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr4:85691800-85716800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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