Variant report

Variant	rs2733840
Chromosome Location	chr12:10545925-10545926
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	JUND	chr12:10545922-10546195	HepG2	liver:	n/a	chr12:10546049-10546058
2	EP300	chr12:10545888-10546408	Hela-S3	cervix:	n/a	chr12:10545921-10545935 chr12:10546122-10546131

Variant related genes	Relation type
KLRK1	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10743888	0.81[EUR][1000 genomes]
rs10743889	0.81[EUR][1000 genomes]
rs1382264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1382265	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1478309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1478310	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1600127	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17549004	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2045876	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2100923	0.81[EUR][1000 genomes]
rs2126888	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2126889	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2246809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2255336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2255353	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2255364	0.93[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2294147	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2417734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2617151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2617152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2617156	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2617157	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2617169	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2617172	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2733845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2733847	1.00[CEU][hapmap];0.82[CHB][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2733848	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2733853	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2734414	0.93[CEU][hapmap];0.85[TSI][hapmap]
rs2734561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2734565	0.89[CHD][hapmap]
rs2927561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4492900	0.81[CEU][hapmap]
rs4764430	0.93[CEU][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6488285	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7307721	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7310643	0.86[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs7314384	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs7397310	0.81[EUR][1000 genomes]
rs7957681	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7958658	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7964772	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832328	chr12:10398071-10620443	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv898759	chr12:10454556-10583365	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv898760	chr12:10492982-10564329	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv898761	chr12:10496724-10564329	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1036390	chr12:10496724-10596720	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv557455	chr12:10508975-10560957	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv898762	chr12:10509383-10564329	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv898763	chr12:10514528-10603670	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv8914	chr12:10532300-10662676	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv557456	chr12:10532326-10698255	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv898764	chr12:10537269-10698255	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv898765	chr12:10537269-10701992	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv898766	chr12:10537269-10722585	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv430461	chr12:10539815-10554033	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv557457	chr12:10545925-10698255	Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2733840	KLRK1	cis	lymphoblastoid	seeQTL
rs2733840	KLRK1	cis	parietal	SCAN
rs2733840	KLRC4	cis	cerebellum	SCAN
rs2733840	KLRC2	cis	cerebellum	SCAN
rs2733840	KLRC4	cis	parietal	SCAN
rs2733840	KLRC4///KLRK1	Cis_1M	lymphoblastoid	RTeQTL
rs2733840	LRRC23	cis	cerebellum	SCAN
rs2733840	KLRK1	Cis_1M	lymphoblastoid	RTeQTL
rs2733840	ZNF384	cis	cerebellum	SCAN
rs2733840	GNB3	cis	cerebellum	SCAN
rs2733840	KLRC4	cis	lesional skin	skin_eQTL
rs2733840	KLRC3	cis	parietal	SCAN
rs2733840	KLRC2	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10519600-10547800	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:10525400-10547200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:10534800-10548800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:10542000-10549200	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr12:10542800-10547800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:10543800-10547600	Enhancers	Hela-S3	cervix
7	chr12:10543800-10547800	Enhancers	Primary B cells from cord blood	blood
8	chr12:10544200-10548200	Enhancers	Primary T cells from cord blood	blood
9	chr12:10544400-10546000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:10544400-10546200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:10544400-10546200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr12:10544400-10547800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr12:10544400-10548200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr12:10544400-10550800	Enhancers	Primary B cells from peripheral blood	blood
15	chr12:10544600-10548800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:10544600-10549000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr12:10544800-10546400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:10544800-10547800	Weak transcription	Adipose Nuclei	Adipose
19	chr12:10545200-10547800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr12:10545200-10548000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:10545400-10546000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:10545400-10546000	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr12:10545400-10546400	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr12:10545400-10546800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr12:10545400-10547000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:10545400-10547000	Weak transcription	Fetal Thymus	thymus
27	chr12:10545400-10548000	Weak transcription	Fetal Lung	lung
28	chr12:10545400-10548000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr12:10545400-10548000	Weak transcription	HSMMtube	muscle
30	chr12:10545400-10548200	Enhancers	NHEK	skin
31	chr12:10545400-10549000	Enhancers	HMEC	breast
32	chr12:10545600-10546200	Enhancers	GM12878-XiMat	blood
33	chr12:10545600-10547000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr12:10545600-10547200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:10545600-10548400	Weak transcription	Esophagus	oesophagus
36	chr12:10545800-10547000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:10545800-10547200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:10545800-10547600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr12:10545800-10547600	Weak transcription	A549	lung
40	chr12:10545800-10547800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:10545800-10547800	Weak transcription	HSMM	muscle
42	chr12:10545800-10547800	Weak transcription	Osteobl	bone

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