Variant report

Variant	rs2165786
Chromosome Location	chr4:85532915-85532916
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:20)

rs_ID	r²[population]
rs1020278	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10446695	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11724113	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11735541	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11929910	0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12108575	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12512391	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12644583	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13102661	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1372971	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];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1443074	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28527489	0.85[YRI][hapmap]
rs2868919	0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap]
rs2868920	0.81[CHB][hapmap];0.83[MEX][hapmap]
rs4568237	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6829806	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7659340	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7677285	0.89[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7678115	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9784491	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]

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
rs2165786	NKX6-1	cis	parietal	SCAN

Chromatin state (count:42 , 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	chr4:85518600-85536200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr4:85518600-85574800	Weak transcription	Stomach Mucosa	stomach
4	chr4:85519000-85536000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:85520400-85559400	Weak transcription	Fetal Heart	heart
6	chr4:85524600-85536400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:85524600-85536400	Weak transcription	Esophagus	oesophagus
8	chr4:85524800-85533800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr4:85525000-85564200	Weak transcription	Placenta	Placenta
10	chr4:85526800-85583000	Weak transcription	Gastric	stomach
11	chr4:85527800-85535400	Strong transcription	Fetal Intestine Small	intestine
12	chr4:85528200-85548200	Weak transcription	Colonic Mucosa	Colon
13	chr4:85528400-85564000	Weak transcription	Fetal Kidney	kidney
14	chr4:85528800-85534600	Weak transcription	Right Ventricle	heart
15	chr4:85529000-85533200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:85529200-85534400	Weak transcription	Lung	lung
17	chr4:85529400-85581600	Weak transcription	Ovary	ovary
18	chr4:85529600-85533800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:85529600-85587600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr4:85529800-85533600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr4:85530400-85533200	Strong transcription	HMEC	breast
22	chr4:85531000-85533200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr4:85531400-85533000	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr4:85531400-85536400	Weak transcription	Fetal Stomach	stomach
25	chr4:85531800-85536200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:85531800-85536200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:85532000-85538000	Weak transcription	Brain Anterior Caudate	brain
28	chr4:85532200-85533200	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr4:85532200-85544200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:85532400-85533000	Weak transcription	Small Intestine	intestine
31	chr4:85532400-85536000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr4:85532400-85536000	Weak transcription	NHEK	skin
33	chr4:85532400-85536600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr4:85532400-85538400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr4:85532400-85540400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr4:85532400-85556800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:85532400-85571200	Weak transcription	Pancreas	Pancrea
38	chr4:85532600-85536000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr4:85532600-85538000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr4:85532600-85538000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr4:85532600-85538000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr4:85532600-85540600	Weak transcription	Fetal Intestine Large	intestine

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