Variant report

Variant	rs1805736
Chromosome Location	chr12:9084931-9084932
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	chr12:9082312-9085096	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:9084849-9086025	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9083802..9086315-chr12:9099049..9101665,2	MCF-7	breast:
2	chr12:9067058..9069439-chr12:9084458..9085959,2	MCF-7	breast:

Variant related genes	Relation type
PHC1	TF binding region
ENSG00000003056	Chromatin interaction
ENSG00000111752	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1049925	0.82[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1073159	0.89[EUR][1000 genomes]
rs10842537	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10842660	0.92[CEU][hapmap];0.85[AMR][1000 genomes]
rs10842662	0.81[AMR][1000 genomes]
rs11047953	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11048023	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11048190	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11048195	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11048264	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11048337	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11048338	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11048344	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11048345	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11048434	0.83[MEX][hapmap]
rs1124402	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11494569	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11494570	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11611106	0.96[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11613242	0.87[EUR][1000 genomes]
rs11613650	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11614970	0.80[EUR][1000 genomes]
rs12371786	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12422905	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12423746	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12423817	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12424026	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12581860	0.80[AMR][1000 genomes]
rs12812913	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12814670	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12815310	0.90[EUR][1000 genomes]
rs12820395	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12821842	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12823100	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12824140	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12824380	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12827055	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12827988	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12828902	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12833375	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1476911	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1805248	0.81[JPT][hapmap]
rs1805721	0.93[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs1805722	0.93[CEU][hapmap]
rs1805723	0.93[CEU][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs1805724	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1805725	0.82[JPT][hapmap]
rs1805727	0.82[JPT][hapmap]
rs1805732	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1805733	0.85[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1805735	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs1805737	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1805745	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1805761	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]
rs1805765	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1805784	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2041624	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2041625	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2080116	0.92[CEU][hapmap];0.85[AMR][1000 genomes]
rs2080117	0.84[AMR][1000 genomes]
rs2110190	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2110191	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2110192	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2110193	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2159961	0.96[CEU][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2377672	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2377673	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2377674	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34285491	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34798934	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35870866	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4254119	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4309200	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6832	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs7299653	0.86[EUR][1000 genomes]
rs7300767	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7301381	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7302417	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7303776	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7306161	0.87[EUR][1000 genomes]
rs7306165	0.86[EUR][1000 genomes]
rs7309922	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7311561	0.82[EUR][1000 genomes]
rs7314942	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7315055	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7957321	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs887782	0.91[CHB][hapmap]
rs933462	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	esv3387088	chr12:9083419-9085279	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv52793	chr12:9083522-9085156	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1805736	KLRG1	cis	Adipose Subcutaneous	GTEx
rs1805736	SPSB2	cis	cerebellum	SCAN
rs1805736	M6PR	cis	cerebellum	SCAN
rs1805736	KLRG1	cis	lymphoblastoid	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9068200-9086400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:9068200-9088800	Weak transcription	Gastric	stomach
3	chr12:9068200-9091400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:9068200-9094200	Weak transcription	Colonic Mucosa	Colon
5	chr12:9068200-9094200	Weak transcription	Lung	lung
6	chr12:9068200-9094200	Weak transcription	Psoas Muscle	Psoas
7	chr12:9068200-9094200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:9068200-9094200	Weak transcription	Small Intestine	intestine
9	chr12:9068200-9100000	Weak transcription	Stomach Mucosa	stomach
10	chr12:9068800-9086400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr12:9069000-9086400	Weak transcription	HepG2	liver
12	chr12:9069000-9094200	Weak transcription	NHLF	lung
13	chr12:9069400-9094000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr12:9069400-9094200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr12:9069600-9092000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:9070400-9092000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:9070400-9092000	Strong transcription	Fetal Muscle Trunk	muscle
18	chr12:9070600-9092000	Strong transcription	Stomach Smooth Muscle	stomach
19	chr12:9070600-9092600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr12:9070600-9092600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr12:9071000-9087800	Strong transcription	Fetal Brain Female	brain
22	chr12:9071000-9092000	Strong transcription	Fetal Muscle Leg	muscle
23	chr12:9071200-9088000	Strong transcription	Primary T cells from cord blood	blood
24	chr12:9071400-9099400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:9071600-9092000	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr12:9071600-9092000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:9071600-9100000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:9072400-9092000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr12:9072400-9094200	Weak transcription	NHEK	skin
30	chr12:9072800-9091000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:9072800-9094200	Weak transcription	HSMM	muscle
32	chr12:9073800-9099800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr12:9074200-9093800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr12:9074400-9094000	Weak transcription	HUVEC	blood vessel
35	chr12:9074600-9094000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr12:9075400-9086400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:9075400-9086400	Weak transcription	Pancreas	Pancrea
38	chr12:9075400-9092000	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr12:9075600-9086000	Weak transcription	NH-A	brain
40	chr12:9075600-9086400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr12:9075600-9087800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:9075800-9086000	Weak transcription	Liver	Liver
43	chr12:9075800-9086200	Weak transcription	Fetal Intestine Large	intestine
44	chr12:9075800-9086400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr12:9075800-9086400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr12:9075800-9089400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:9075800-9094000	Weak transcription	HMEC	breast
48	chr12:9076000-9085800	Weak transcription	HSMMtube	muscle
49	chr12:9076000-9086400	Weak transcription	A549	lung
50	chr12:9076000-9091400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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