Variant report

Variant	rs12502294
Chromosome Location	chr4:85703188-85703189
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12500519	0.82[EUR][1000 genomes]
rs12502409	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	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13118671	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.82[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]
rs16995920	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17009317	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap]
rs17009334	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
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	0.81[EUR][1000 genomes]
rs36036245	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3747680	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4590017	0.85[CEU][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap]
rs6816534	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6825852	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6829807	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6838727	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6847067	0.90[JPT][hapmap]
rs6847564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6858666	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs72664928	0.82[EUR][1000 genomes]
rs7685537	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs7692223	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs7695054	0.82[EUR][1000 genomes]

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
rs12502294	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:102 , 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	chr4:85657000-85704200	Weak transcription	Psoas Muscle	Psoas
3	chr4:85664000-85703400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr4:85664000-85703600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:85664200-85703600	Weak transcription	Right Ventricle	heart
6	chr4:85668600-85703800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:85669600-85703600	Weak transcription	Aorta	Aorta
8	chr4:85672400-85707000	Weak transcription	Colonic Mucosa	Colon
9	chr4:85672800-85703600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:85672800-85703600	Weak transcription	Esophagus	oesophagus
11	chr4:85672800-85703600	Weak transcription	NHLF	lung
12	chr4:85673200-85703600	Weak transcription	HepG2	liver
13	chr4:85675200-85703600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr4:85675600-85703600	Weak transcription	Fetal Brain Male	brain
15	chr4:85677200-85707200	Weak transcription	NHEK	skin
16	chr4:85678400-85703600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:85683800-85732000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr4:85684800-85725000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr4:85688800-85725600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:85689600-85717200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:85689800-85703600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr4:85690000-85722000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:85690800-85725600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr4:85691000-85724800	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:85691600-85712200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:85691600-85718400	Strong transcription	Placenta	Placenta
27	chr4:85691800-85703800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:85691800-85716800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:85692000-85710400	Strong transcription	HUVEC	blood vessel
30	chr4:85692800-85709800	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr4:85694400-85711200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr4:85694800-85704600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:85694800-85704800	Weak transcription	Fetal Heart	heart
34	chr4:85695200-85718000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:85696200-85703600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr4:85696400-85757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr4:85697400-85705400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr4:85697400-85709200	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr4:85697400-85772800	Weak transcription	Small Intestine	intestine
40	chr4:85697800-85709000	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr4:85697800-85709600	Strong transcription	Fetal Lung	lung
42	chr4:85698000-85724600	Strong transcription	Liver	Liver
43	chr4:85699000-85710000	Strong transcription	Fetal Brain Female	brain
44	chr4:85699200-85703200	Weak transcription	Fetal Kidney	kidney
45	chr4:85699400-85703600	Weak transcription	Rectal Smooth Muscle	rectum
46	chr4:85699600-85703600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:85699800-85705400	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr4:85700000-85716200	Strong transcription	Adipose Nuclei	Adipose
49	chr4:85700200-85724600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr4:85700400-85709000	Strong transcription	Brain Cingulate Gyrus	brain

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