Variant report

Variant	rs6838727
Chromosome Location	chr4:85656350-85656351
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11725121	0.80[EUR][1000 genomes]
rs12500519	0.82[EUR][1000 genomes]
rs12502294	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12502409	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12511112	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs13108722	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13118671	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs1484661	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1508670	0.90[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap]
rs16995920	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17009317	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs17009334	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[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	0.81[EUR][1000 genomes]
rs36036245	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3747680	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6816534	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6825852	1.00[ASW][hapmap];1.00[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];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6829807	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6847067	0.90[JPT][hapmap]
rs6847564	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6858666	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs72664928	0.82[EUR][1000 genomes]
rs7685537	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs7695054	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6838727	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85604400-85674800	Weak transcription	Small Intestine	intestine
2	chr4:85615000-85677600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:85619200-85726000	Weak transcription	Hela-S3	cervix
4	chr4:85620800-85663400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:85629200-85662400	Weak transcription	Colonic Mucosa	Colon
6	chr4:85630000-85656400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:85630000-85659000	Weak transcription	Right Ventricle	heart
8	chr4:85630200-85656400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:85632600-85658200	Weak transcription	A549	lung
10	chr4:85633400-85667800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:85636400-85701200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:85637400-85658400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:85640200-85663200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:85642800-85656400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:85642800-85656400	Weak transcription	Aorta	Aorta
16	chr4:85642800-85656400	Weak transcription	Pancreas	Pancrea
17	chr4:85642800-85658200	Weak transcription	Fetal Stomach	stomach
18	chr4:85642800-85658200	Weak transcription	Left Ventricle	heart
19	chr4:85642800-85658200	Weak transcription	Lung	lung
20	chr4:85642800-85659000	Weak transcription	Fetal Intestine Small	intestine
21	chr4:85642800-85660000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr4:85642800-85668000	Weak transcription	Spleen	Spleen
23	chr4:85642800-85678000	Weak transcription	Gastric	stomach
24	chr4:85643000-85659000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:85643200-85656400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:85644200-85660400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr4:85644400-85656400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:85645000-85658000	Weak transcription	Brain Angular Gyrus	brain
29	chr4:85646400-85656400	Weak transcription	Esophagus	oesophagus
30	chr4:85646400-85663400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr4:85648000-85676200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr4:85650200-85657800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:85651000-85671400	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr4:85651000-85673000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr4:85651000-85673200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr4:85651000-85676800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr4:85651000-85678600	Strong transcription	Placenta	Placenta
38	chr4:85651200-85664400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:85651400-85658800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:85652200-85661600	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr4:85652200-85664000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:85652200-85664800	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr4:85652200-85665000	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr4:85652200-85665000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr4:85652200-85665200	Strong transcription	Adipose Nuclei	Adipose
46	chr4:85652200-85670000	Strong transcription	Liver	Liver
47	chr4:85652200-85678400	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr4:85652200-85678400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:85652200-85679200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:85652400-85661000	Strong transcription	Colon Smooth Muscle	Colon

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