Variant report

Variant	rs6853486
Chromosome Location	chr4:85540814-85540815
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10000060	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10446678	0.87[ASN][1000 genomes]
rs12511112	0.91[CEU][hapmap];0.91[MEX][hapmap]
rs13110728	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17009168	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.99[ASN][1000 genomes]
rs17367226	1.00[YRI][hapmap]
rs1838038	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2120091	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2218323	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs3098928	0.91[CEU][hapmap];0.91[MEX][hapmap]
rs35928242	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3804180	1.00[YRI][hapmap]
rs6842038	0.82[CHB][hapmap]
rs6847067	0.82[CEU][hapmap]
rs6858666	0.83[CEU][hapmap];0.91[MEX][hapmap]
rs7685537	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs7689916	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830333	chr4:85520643-85545644	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6853486	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85515400-85544400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:85518600-85574800	Weak transcription	Stomach Mucosa	stomach
3	chr4:85520400-85559400	Weak transcription	Fetal Heart	heart
4	chr4:85525000-85564200	Weak transcription	Placenta	Placenta
5	chr4:85526800-85583000	Weak transcription	Gastric	stomach
6	chr4:85528200-85548200	Weak transcription	Colonic Mucosa	Colon
7	chr4:85528400-85564000	Weak transcription	Fetal Kidney	kidney
8	chr4:85529400-85581600	Weak transcription	Ovary	ovary
9	chr4:85529600-85587600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr4:85532200-85544200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr4:85532400-85556800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:85532400-85571200	Weak transcription	Pancreas	Pancrea
13	chr4:85533200-85541400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:85536400-85541800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:85536600-85552000	Weak transcription	NHEK	skin
16	chr4:85536800-85544800	Weak transcription	Esophagus	oesophagus
17	chr4:85536800-85546400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr4:85536800-85556600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:85536800-85570200	Weak transcription	Fetal Stomach	stomach
20	chr4:85537200-85568600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:85537600-85542400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:85538000-85541000	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr4:85538600-85568600	Weak transcription	Brain Anterior Caudate	brain
24	chr4:85539000-85550600	Weak transcription	HMEC	breast
25	chr4:85539200-85541200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:85539200-85560200	Weak transcription	Left Ventricle	heart
27	chr4:85539800-85541000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr4:85540000-85546000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr4:85540000-85562000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr4:85540200-85544200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr4:85540200-85544200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:85540200-85547400	Strong transcription	Fetal Intestine Small	intestine
33	chr4:85540400-85556000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr4:85540600-85541000	Strong transcription	Fetal Intestine Large	intestine
35	chr4:85540600-85544000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr4:85540800-85542200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:85540800-85558000	Weak transcription	Rectal Mucosa Donor 29	rectum

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