Variant report

Variant	rs12817345
Chromosome Location	chr12:10550007-10550008
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	chr12:10547736..10550018-chr12:10555798..10557891,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLRD1-1	chr12:10548778-10551105	ENSG00000245648

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12816829	0.88[EUR][1000 genomes]
rs12819494	0.88[EUR][1000 genomes]
rs12821887	0.88[EUR][1000 genomes]
rs12824244	0.88[EUR][1000 genomes]
rs12824247	0.88[EUR][1000 genomes]
rs12825500	0.88[EUR][1000 genomes]
rs12827347	0.88[EUR][1000 genomes]
rs12830618	0.88[EUR][1000 genomes]
rs17513965	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17513986	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35968979	0.88[EUR][1000 genomes]
rs71450040	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71450042	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71450043	0.88[EUR][1000 genomes]
rs71450045	0.88[EUR][1000 genomes]
rs728010	0.88[EUR][1000 genomes]
rs728011	0.88[EUR][1000 genomes]
rs7955196	0.88[EUR][1000 genomes]
rs7980470	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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
17	nsv557458	chr12:10546140-10698255	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
18	nsv1051292	chr12:10547900-10596720	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12817345	KLRC3,KLRC2	cis	brain	BrainEAC
rs12817345	KLRC3,KLRC2	cis	substantia nigra	BrainEAC
rs12817345	KLRC3,KLRC2	cis	frontal cortex	BrainEAC
rs12817345	KLRC3,KLRC2	cis	intralobular white matter	BrainEAC
rs12817345	KLRC3,KLRC2	cis	hippocampus	BrainEAC

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10544400-10550800	Enhancers	Primary B cells from peripheral blood	blood
2	chr12:10547800-10559400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:10548400-10550600	Active TSS	Hela-S3	cervix
4	chr12:10548600-10550200	Enhancers	Primary T cells fromperipheralblood	blood
5	chr12:10548600-10550200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr12:10548600-10550400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:10548600-10550600	Enhancers	Primary T cells from cord blood	blood
8	chr12:10548600-10550600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:10548600-10557400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:10548600-10564000	Weak transcription	Brain Angular Gyrus	brain
11	chr12:10548800-10551200	Enhancers	Primary B cells from cord blood	blood
12	chr12:10548800-10551600	Weak transcription	NHEK	skin
13	chr12:10549000-10553000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr12:10549200-10550800	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr12:10549200-10559400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:10549400-10550400	Enhancers	A549	lung
17	chr12:10549600-10550200	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr12:10549800-10550200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr12:10549800-10550200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:10549800-10550600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:10550000-10550200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:10550000-10550200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr12:10550000-10550200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:10550000-10550200	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr12:10550000-10550200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:10550000-10550200	Enhancers	Muscle Satellite Cultured Cells	--
27	chr12:10550000-10550200	Enhancers	Fetal Thymus	thymus
28	chr12:10550000-10550200	Enhancers	HMEC	breast
29	chr12:10550000-10550400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr12:10550000-10550800	Enhancers	Small Intestine	intestine

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