Variant report

Variant	rs1372971
Chromosome Location	chr4:85571339-85571340
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:85564288..85566182-chr4:85568579..85571461,2	K562	blood:
2	chr4:85570877..85573206-chr4:85576322..85578713,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10014792	0.83[ASW][hapmap];0.83[YRI][hapmap]
rs10019164	0.81[EUR][1000 genomes]
rs1020278	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.87[ASN][1000 genomes]
rs10446695	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11097023	0.91[GIH][hapmap];0.87[MEX][hapmap]
rs11724113	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11735541	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11929910	0.92[CEU][hapmap];0.86[CHB][hapmap]
rs12108575	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12512391	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12644583	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1443074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1946998	0.80[MEX][hapmap]
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];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2868917	0.83[MEX][hapmap]
rs2868919	0.92[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap]
rs2868920	0.81[CHB][hapmap];0.92[MEX][hapmap]
rs4449405	0.89[GIH][hapmap];0.92[MEX][hapmap]
rs4568237	0.86[EUR][1000 genomes];0.80[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];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7659340	0.92[CEU][hapmap];0.86[CHB][hapmap]
rs7677285	0.89[CEU][hapmap];0.86[CHB][hapmap]
rs9784491	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]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1372971	NKX6-1	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85518600-85574800	Weak transcription	Stomach Mucosa	stomach
2	chr4:85526800-85583000	Weak transcription	Gastric	stomach
3	chr4:85529400-85581600	Weak transcription	Ovary	ovary
4	chr4:85529600-85587600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:85544600-85572400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:85545200-85576400	Weak transcription	Esophagus	oesophagus
7	chr4:85556600-85572200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:85564800-85587800	Weak transcription	Fetal Kidney	kidney
9	chr4:85568400-85573200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:85568600-85572200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:85568600-85572400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:85568600-85573200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:85568600-85574000	Strong transcription	Duodenum Mucosa	Duodenum
14	chr4:85568800-85578600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:85568800-85589600	Weak transcription	Brain Angular Gyrus	brain
16	chr4:85569200-85571600	Strong transcription	HMEC	breast
17	chr4:85569200-85572800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:85569200-85587200	Weak transcription	Brain Anterior Caudate	brain
19	chr4:85569600-85577600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr4:85569600-85579200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:85569600-85582600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr4:85569800-85575000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:85570000-85573400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr4:85570400-85572800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr4:85570600-85571400	Strong transcription	NHEK	skin
26	chr4:85570600-85571600	Strong transcription	Fetal Intestine Small	intestine
27	chr4:85570600-85572400	Strong transcription	Fetal Intestine Large	intestine
28	chr4:85570800-85571400	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr4:85570800-85571600	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr4:85570800-85572200	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr4:85571000-85571800	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr4:85571000-85572000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:85571000-85572000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr4:85571000-85572200	Weak transcription	Fetal Lung	lung
35	chr4:85571000-85572600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:85571000-85588800	Weak transcription	Left Ventricle	heart
37	chr4:85571000-85592400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr4:85571200-85572000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr4:85571200-85572400	Weak transcription	Fetal Heart	heart
40	chr4:85571200-85581400	Weak transcription	Rectal Mucosa Donor 31	rectum

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