Variant report

Variant	rs7969985
Chromosome Location	chr12:10535456-10535457
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	chr12:10534850..10537741-chr12:10540764..10542364,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213809	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs12423025	0.85[EUR][1000 genomes]
rs12423464	0.85[EUR][1000 genomes]
rs12424871	1.00[EUR][1000 genomes]
rs12425047	0.85[EUR][1000 genomes]
rs12425840	0.81[EUR][1000 genomes]
rs12426187	1.00[EUR][1000 genomes]
rs12427017	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12816829	0.82[ASN][1000 genomes]
rs12818744	0.84[ASN][1000 genomes]
rs12819494	0.89[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs12821887	0.89[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs12824244	0.84[ASN][1000 genomes]
rs12824247	0.84[ASN][1000 genomes]
rs12825500	0.84[ASN][1000 genomes]
rs12826560	0.89[CHB][hapmap];0.85[JPT][hapmap];0.80[YRI][hapmap];0.84[ASN][1000 genomes]
rs12827347	0.84[ASN][1000 genomes]
rs12830618	0.88[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs1971939	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2253365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35968979	0.82[ASN][1000 genomes]
rs3736060	0.82[ASN][1000 genomes]
rs3809215	1.00[EUR][1000 genomes]
rs3809216	1.00[EUR][1000 genomes]
rs3983616	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57106039	1.00[EUR][1000 genomes]
rs59372234	1.00[EUR][1000 genomes]
rs60018231	1.00[EUR][1000 genomes]
rs60078099	1.00[EUR][1000 genomes]
rs60248367	1.00[EUR][1000 genomes]
rs61571638	1.00[EUR][1000 genomes]
rs6488287	1.00[EUR][1000 genomes]
rs6488290	0.85[EUR][1000 genomes]
rs7131960	0.85[EUR][1000 genomes]
rs7134846	1.00[EUR][1000 genomes]
rs71450043	0.82[ASN][1000 genomes]
rs71450045	0.82[ASN][1000 genomes]
rs72475439	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72475440	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72475441	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72475442	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72475450	1.00[EUR][1000 genomes]
rs72475451	1.00[EUR][1000 genomes]
rs72475452	1.00[EUR][1000 genomes]
rs728010	0.89[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs728011	0.82[ASN][1000 genomes]
rs7301325	0.85[EUR][1000 genomes]
rs7309785	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs74060400	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74062006	0.84[EUR][1000 genomes]
rs74062025	1.00[EUR][1000 genomes]
rs74062026	1.00[EUR][1000 genomes]
rs7952993	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7953443	1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[EUR][1000 genomes]
rs7955196	0.89[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7962112	0.89[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs7972757	0.89[CHB][hapmap];0.86[JPT][hapmap];0.94[YRI][hapmap];0.84[ASN][1000 genomes]
rs7980470	0.89[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7969985	KLRK1	cis	multi-tissue	Pritchard

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10518400-10537000	Weak transcription	Left Ventricle	heart
2	chr12:10519600-10547800	Weak transcription	Colon Smooth Muscle	Colon
3	chr12:10523000-10536000	Weak transcription	Ovary	ovary
4	chr12:10525400-10547200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:10527600-10538600	Weak transcription	Brain Hippocampus Middle	brain
6	chr12:10531200-10544400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr12:10533200-10541400	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:10533600-10538000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:10533600-10538600	Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr12:10533800-10535800	Weak transcription	Primary T cells from cord blood	blood
11	chr12:10533800-10537800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:10533800-10538200	Weak transcription	Fetal Intestine Large	intestine
13	chr12:10533800-10539000	Weak transcription	Fetal Intestine Small	intestine
14	chr12:10533800-10544600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:10534200-10535800	Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr12:10534600-10544600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:10534800-10535600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:10534800-10537600	Weak transcription	Osteobl	bone
19	chr12:10534800-10537800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
20	chr12:10534800-10542000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr12:10534800-10544400	Weak transcription	NHEK	skin
22	chr12:10534800-10548800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:10535000-10537600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:10535200-10536200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr12:10535200-10536800	Weak transcription	Primary B cells from cord blood	blood
26	chr12:10535200-10537400	Weak transcription	Hela-S3	cervix

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