Variant report

Variant	rs9784491
Chromosome Location	chr4:85560271-85560272
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10014792	0.83[ASW][hapmap];1.00[YRI][hapmap]
rs1020278	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10446695	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11097023	0.91[GIH][hapmap]
rs11724113	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11735541	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11929910	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[YRI][hapmap]
rs12108575	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12512391	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12644583	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13102661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1372971	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1443074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2868919	0.92[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs2868920	0.81[CHB][hapmap];0.83[MEX][hapmap]
rs4449405	0.89[GIH][hapmap];0.83[MEX][hapmap]
rs4568237	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6829806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7659340	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[YRI][hapmap]
rs7677285	0.89[CEU][hapmap];0.86[CHB][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9784491	NKX6-1	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85518600-85574800	Weak transcription	Stomach Mucosa	stomach
2	chr4:85525000-85564200	Weak transcription	Placenta	Placenta
3	chr4:85526800-85583000	Weak transcription	Gastric	stomach
4	chr4:85528400-85564000	Weak transcription	Fetal Kidney	kidney
5	chr4:85529400-85581600	Weak transcription	Ovary	ovary
6	chr4:85529600-85587600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr4:85532400-85571200	Weak transcription	Pancreas	Pancrea
8	chr4:85536800-85570200	Weak transcription	Fetal Stomach	stomach
9	chr4:85537200-85568600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:85538600-85568600	Weak transcription	Brain Anterior Caudate	brain
11	chr4:85540000-85562000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr4:85541000-85561800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr4:85544200-85561600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:85544600-85564400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr4:85544600-85568000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:85544600-85572400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr4:85545200-85576400	Weak transcription	Esophagus	oesophagus
18	chr4:85546600-85570400	Weak transcription	Small Intestine	intestine
19	chr4:85547000-85562400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr4:85554200-85562000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:85555200-85568800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr4:85556600-85570400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr4:85556600-85572200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr4:85556800-85570600	Weak transcription	Lung	lung
25	chr4:85556800-85570600	Weak transcription	NHEK	skin
26	chr4:85557400-85566800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr4:85557600-85569200	Weak transcription	HMEC	breast
28	chr4:85558200-85561000	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr4:85558200-85565400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:85558400-85560400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr4:85558400-85562800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr4:85558800-85562200	Weak transcription	Fetal Intestine Small	intestine
33	chr4:85558800-85562400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:85559000-85562000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:85559000-85562000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:85559400-85562000	Weak transcription	Fetal Intestine Large	intestine
37	chr4:85559800-85567800	Weak transcription	Fetal Heart	heart
38	chr4:85560000-85560400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr4:85560200-85560400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr4:85560200-85560600	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr4:85560200-85560600	Enhancers	Left Ventricle	heart
42	chr4:85560200-85560600	Enhancers	Psoas Muscle	Psoas
43	chr4:85560200-85560800	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr4:85560200-85560800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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