Variant report

Variant	rs6076060
Chromosome Location	chr20:23345069-23345070
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:23344914-23345091	GM12878	blood:	n/a	n/a
2	POLR2A	chr20:23341279-23355011	HepG2	liver:	n/a	n/a
3	POLR2A	chr20:23341069-23355530	K562	blood:	n/a	n/a
4	POLR2A	chr20:23340935-23347328	IMR90	lung:	n/a	n/a
5	POLR2A	chr20:23345058-23345285	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:38978307..38979883-chr20:23342389..23345213,2	MCF-7	breast:
2	chr20:23344681..23346860-chr20:23360081..23363046,2	MCF-7	breast:
3	chr20:23338809..23345308-chr20:23399768..23403114,12	K562	blood:

Variant related genes	Relation type
GZF1	TF binding region
ENSG00000125814	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000201728	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11908625	0.93[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap]
rs1203994	0.95[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2153986	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2281433	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2424556	0.91[LWK][hapmap]
rs2424557	0.93[LWK][hapmap]
rs56917308	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60130293	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6036381	0.84[ASN][1000 genomes]
rs6036387	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036388	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036393	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036394	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036395	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036396	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6036400	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036402	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048721	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6048724	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6048726	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6048727	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6048747	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs6048748	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048749	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048751	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048764	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048773	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6048780	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6048782	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6048783	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6048785	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6048787	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6048789	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6048791	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6048792	0.85[ASN][1000 genomes]
rs6048793	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6048794	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6076052	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6076061	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076069	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6083079	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6083082	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083091	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083109	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6083117	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6083120	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6083125	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6106650	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6106652	0.83[ASN][1000 genomes]
rs6114053	1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6114078	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6114086	0.93[CHD][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs73303309	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73319497	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7351246	0.82[TSI][hapmap]
rs7361799	0.81[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6076060	CXCL2	trans	brain	seeQTL
rs6076060	CXCL11	trans	brain	seeQTL
rs6076060	CXCL10	trans	brain	seeQTL
rs6076060	CSF3	trans	brain	seeQTL
rs6076060	IL8	trans	brain	seeQTL
rs6076060	CXCL1	trans	brain	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23342400-23352600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:23343600-23345200	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr20:23344000-23345200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr20:23344000-23345200	Enhancers	Adipose Nuclei	Adipose
5	chr20:23344000-23345200	Enhancers	Right Atrium	heart
6	chr20:23344000-23345400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr20:23344000-23345400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr20:23344000-23346000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr20:23344000-23347600	Enhancers	Primary T cells fromperipheralblood	blood
10	chr20:23344000-23392600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr20:23344200-23345200	Weak transcription	Aorta	Aorta
12	chr20:23344200-23345200	Weak transcription	Brain Germinal Matrix	brain
13	chr20:23344200-23345400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr20:23344200-23345800	Weak transcription	Ovary	ovary
15	chr20:23344200-23346000	Weak transcription	Fetal Brain Male	brain
16	chr20:23344200-23346600	Genic enhancers	Spleen	Spleen
17	chr20:23344400-23345200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr20:23344400-23345200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr20:23344400-23345200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr20:23344400-23345200	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr20:23344400-23345200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr20:23344400-23345200	Weak transcription	Colon Smooth Muscle	Colon
23	chr20:23344400-23345200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr20:23344400-23345200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr20:23344400-23345200	Weak transcription	NHDF-Ad	bronchial
26	chr20:23344400-23345400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr20:23344400-23345400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr20:23344400-23345400	Weak transcription	Esophagus	oesophagus
29	chr20:23344400-23345400	Weak transcription	Placenta	Placenta
30	chr20:23344400-23345400	Weak transcription	Lung	lung
31	chr20:23344400-23345400	Weak transcription	Pancreas	Pancrea
32	chr20:23344400-23345800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr20:23344400-23346200	Weak transcription	Small Intestine	intestine
34	chr20:23344400-23346400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr20:23344400-23346400	Weak transcription	Primary B cells from cord blood	blood
36	chr20:23344400-23346400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr20:23344400-23346400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr20:23344400-23346400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr20:23344400-23346400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr20:23344400-23346600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr20:23344400-23346600	Strong transcription	Brain Angular Gyrus	brain
42	chr20:23344400-23346600	Weak transcription	Psoas Muscle	Psoas
43	chr20:23344400-23346600	Weak transcription	Hela-S3	cervix
44	chr20:23344400-23347200	Genic enhancers	Dnd41	blood
45	chr20:23344400-23347800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr20:23344400-23349200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr20:23344400-23350200	Weak transcription	Fetal Kidney	kidney
48	chr20:23344600-23345200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr20:23344600-23345400	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr20:23344600-23345400	Weak transcription	HSMMtube	muscle

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