Variant report

Variant	rs11724113
Chromosome Location	chr4:85574833-85574834
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10019164	0.81[EUR][1000 genomes]
rs1020278	1.00[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10446695	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11097023	0.94[GIH][hapmap];0.87[MEX][hapmap]
rs11735541	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11929910	0.88[CEU][hapmap]
rs12108575	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12512391	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12644583	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13102661	0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1372971	0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1443074	0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2165786	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2868917	0.83[MEX][hapmap]
rs2868919	0.89[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap]
rs2868920	0.92[MEX][hapmap]
rs4449405	0.92[GIH][hapmap];0.83[MEX][hapmap]
rs4568237	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6829806	0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7659340	0.89[CEU][hapmap]
rs7677285	0.85[CEU][hapmap]
rs9784491	0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11724113	NKX6-1	cis	parietal	SCAN
rs11724113	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85526800-85583000	Weak transcription	Gastric	stomach
2	chr4:85529400-85581600	Weak transcription	Ovary	ovary
3	chr4:85529600-85587600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:85545200-85576400	Weak transcription	Esophagus	oesophagus
5	chr4:85564800-85587800	Weak transcription	Fetal Kidney	kidney
6	chr4:85568800-85578600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:85568800-85589600	Weak transcription	Brain Angular Gyrus	brain
8	chr4:85569200-85587200	Weak transcription	Brain Anterior Caudate	brain
9	chr4:85569600-85577600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr4:85569600-85579200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:85569600-85582600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr4:85569800-85575000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:85571000-85588800	Weak transcription	Left Ventricle	heart
14	chr4:85571000-85592400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr4:85571200-85581400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr4:85571400-85576000	Weak transcription	NHEK	skin
17	chr4:85571400-85579200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:85571600-85576000	Weak transcription	Fetal Intestine Small	intestine
19	chr4:85572200-85587800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:85572400-85577800	Weak transcription	Fetal Intestine Large	intestine
21	chr4:85572400-85579200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:85572800-85576000	Weak transcription	HMEC	breast
23	chr4:85573200-85578800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:85573200-85588600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:85573400-85578800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:85573400-85582400	Weak transcription	Fetal Heart	heart
27	chr4:85574000-85578600	Weak transcription	Duodenum Mucosa	Duodenum

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