Variant report

Variant	rs1805761
Chromosome Location	chr12:9099533-9099534
allele	A/G
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	BHLHE40	chr12:9099466-9099666	GM12878	blood:	n/a	n/a
2	NFATC1	chr12:9099066-9099614	GM12878	blood:	n/a	n/a
3	RUNX3	chr12:9099300-9099733	GM12878	blood:	n/a	chr12:9099565-9099574 chr12:9099565-9099574
4	TCF12	chr12:9099365-9099554	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:9098618-9099635	H1-hESC	embryonic stem cell:	n/a	n/a
6	NFIC	chr12:9099213-9099704	GM12878	blood:	n/a	n/a
7	CUX1	chr12:9099191-9099635	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:9099512-9099559	K562	blood:	n/a	n/a
9	WRNIP1	chr12:9099302-9100626	GM12878	blood:	n/a	n/a
10	EBF1	chr12:9099209-9099621	GM12878	blood:	n/a	n/a
11	ATF2	chr12:9099102-9099686	GM12878	blood:	n/a	n/a
12	RUNX3	chr12:9099243-9099804	GM12878	blood:	n/a	chr12:9099565-9099574 chr12:9099565-9099574
13	BATF	chr12:9099277-9099680	GM12878	blood:	n/a	n/a
14	RELA	chr12:9099210-9099730	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:9065401..9068009-chr12:9098811..9103435,5	MCF-7	breast:
2	chr12:9066826..9070397-chr12:9099293..9102558,3	K562	blood:
3	chr12:9083802..9086315-chr12:9099049..9101665,2	MCF-7	breast:
4	chr12:9096830..9100498-chr12:9102068..9104762,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-A2M-3	chr12:9099453-9099601	ucscGeneNc_uc009zgh_1

Variant related genes	Relation type
M6PR	TF binding region
KLRG1	TF binding region
ENSG00000111752	Chromatin interaction
ENSG00000139187	Chromatin interaction
ENSG00000003056	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10129061	0.95[CHB][hapmap]
rs10400516	0.81[ASN][1000 genomes]
rs1049925	0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1073159	0.84[EUR][1000 genomes]
rs10842537	0.86[EUR][1000 genomes]
rs10842660	0.92[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10842662	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11047953	0.86[EUR][1000 genomes]
rs11048023	0.90[EUR][1000 genomes]
rs11048190	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11048195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11048264	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11048337	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11048338	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11048344	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11048345	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11048434	0.91[JPT][hapmap];0.83[MEX][hapmap]
rs1124402	0.85[EUR][1000 genomes]
rs11494569	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11494570	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11611106	0.96[CEU][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs11613242	0.82[EUR][1000 genomes]
rs11613650	0.85[EUR][1000 genomes]
rs11614202	0.90[ASN][1000 genomes]
rs12371786	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12422905	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12423746	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12423817	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12424026	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12581860	0.84[AMR][1000 genomes]
rs12812913	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12814670	0.85[EUR][1000 genomes]
rs12815310	0.85[EUR][1000 genomes]
rs12820395	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12821842	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12823100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12824140	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12824212	0.91[JPT][hapmap]
rs12824380	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12827055	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12827988	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12828902	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12833375	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1476911	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1805248	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1805677	0.91[JPT][hapmap]
rs1805719	0.91[JPT][hapmap]
rs1805721	0.92[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1805722	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1805723	0.92[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1805724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1805725	0.95[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1805727	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1805732	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805733	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1805735	0.91[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs1805736	0.92[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1805737	0.93[EUR][1000 genomes]
rs1805745	0.86[EUR][1000 genomes]
rs1805754	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs1805765	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1805784	0.86[EUR][1000 genomes]
rs2041624	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2041625	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2080116	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2080117	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2110190	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2110191	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2110192	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2110193	0.85[EUR][1000 genomes]
rs2159961	0.96[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs2377671	0.80[ASN][1000 genomes]
rs2377672	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2377673	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2377674	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34285491	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34798934	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35870866	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4254119	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4309200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4639983	0.95[CHB][hapmap]
rs6832	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs7299653	0.81[EUR][1000 genomes]
rs7300767	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7301381	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7302417	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7303776	0.85[EUR][1000 genomes]
rs7306161	0.82[EUR][1000 genomes]
rs7306165	0.81[EUR][1000 genomes]
rs7309922	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7314942	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7315055	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7957321	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs933462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs987917	0.95[CHB][hapmap];0.80[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	nsv832327	chr12:9081779-9246220	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1805761	KLRG1	cis	lymphoblastoid	seeQTL
rs1805761	SPSB2	cis	cerebellum	SCAN
rs1805761	M6PR	cis	cerebellum	SCAN
rs1805761	KLRG1	cis	multi-tissue	Pritchard
rs1805761	TAS2R46	cis	cerebellum	SCAN
rs1805761	KLRG1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9068200-9100000	Weak transcription	Stomach Mucosa	stomach
2	chr12:9071600-9100000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:9073800-9099800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr12:9087000-9101200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:9091600-9101200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:9093600-9099600	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr12:9093800-9099600	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr12:9093800-9099600	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr12:9093800-9099600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:9093800-9099600	Strong transcription	Fetal Muscle Trunk	muscle
11	chr12:9093800-9099600	Strong transcription	A549	lung
12	chr12:9093800-9099800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:9094000-9099600	Strong transcription	Brain Germinal Matrix	brain
14	chr12:9094000-9099800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:9094000-9099800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:9094000-9099800	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr12:9094000-9099800	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr12:9094000-9100200	Strong transcription	Fetal Muscle Leg	muscle
19	chr12:9096600-9099600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:9096600-9100000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr12:9096600-9100200	Weak transcription	Psoas Muscle	Psoas
22	chr12:9096600-9101200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:9097000-9100000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:9098000-9099600	Weak transcription	Small Intestine	intestine
25	chr12:9098000-9101400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:9098200-9099600	Weak transcription	Fetal Intestine Small	intestine
27	chr12:9098200-9099800	Weak transcription	Brain Angular Gyrus	brain
28	chr12:9098200-9100000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr12:9098200-9100000	Weak transcription	Spleen	Spleen
30	chr12:9098200-9100000	Weak transcription	NHEK	skin
31	chr12:9098200-9100400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:9098200-9100400	Weak transcription	HUVEC	blood vessel
33	chr12:9098200-9100800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr12:9098200-9101000	Weak transcription	Right Ventricle	heart
35	chr12:9098200-9101200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr12:9098200-9101200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr12:9098200-9101200	Weak transcription	Colonic Mucosa	Colon
38	chr12:9098200-9101200	Weak transcription	Gastric	stomach
39	chr12:9098200-9101200	Weak transcription	Pancreas	Pancrea
40	chr12:9098200-9101400	Weak transcription	Aorta	Aorta
41	chr12:9098200-9101400	Weak transcription	Esophagus	oesophagus
42	chr12:9098400-9100000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:9098400-9100000	Weak transcription	Brain Substantia Nigra	brain
44	chr12:9098400-9100000	Weak transcription	HSMMtube	muscle
45	chr12:9098400-9101000	Weak transcription	Fetal Stomach	stomach
46	chr12:9098400-9101000	Weak transcription	HSMM	muscle
47	chr12:9098400-9101200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:9098400-9101200	Weak transcription	Ovary	ovary
49	chr12:9098400-9101400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr12:9098400-9101400	Weak transcription	Lung	lung

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