Variant report

Variant	rs2255336
Chromosome Location	chr12:10532326-10532327
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLRD1-1	chr12:10532301-10532435	ENSG00000245648

Extended variants
information (count: 62 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1049172	0.92[MEX][hapmap];0.86[YRI][hapmap]
rs10743888	0.82[EUR][1000 genomes]
rs10743889	0.81[EUR][1000 genomes]
rs12318583	0.81[ASN][1000 genomes]
rs1351113	0.92[MEX][hapmap];0.86[YRI][hapmap]
rs1382264	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1382265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1478309	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1478310	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1600127	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17549004	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1841958	0.82[JPT][hapmap]
rs2045876	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2100923	0.81[EUR][1000 genomes]
rs2126888	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2126889	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2246809	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2255353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255364	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294147	0.88[CHB][hapmap]
rs2417734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2617150	0.82[JPT][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs2617151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2617157	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2617169	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2617172	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2733840	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]
rs2733845	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2733847	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2733848	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2733851	0.81[ASN][1000 genomes]
rs2733852	0.86[CHD][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.83[YRI][hapmap];0.81[ASN][1000 genomes]
rs2733853	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2734414	0.93[CEU][hapmap];0.89[TSI][hapmap]
rs2734561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2734565	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs2927561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4415856	0.81[MKK][hapmap];0.83[TSI][hapmap]
rs4492900	0.81[CEU][hapmap]
rs4764430	0.93[CEU][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs6488285	0.90[EUR][1000 genomes]
rs7301582	0.82[TSI][hapmap]
rs7307721	0.90[EUR][1000 genomes]
rs7310643	0.86[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs7314384	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs7397310	0.82[EUR][1000 genomes]
rs7957681	0.90[EUR][1000 genomes]
rs7958658	0.90[EUR][1000 genomes]
rs7964772	0.90[EUR][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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2255336	LRRC23	cis	cerebellum	SCAN
rs2255336	KLRC4	cis	cerebellum	SCAN
rs2255336	KLRC4	cis	parietal	SCAN
rs2255336	KLRC2	cis	parietal	SCAN
rs2255336	KLRK1	Cis_1M	lymphoblastoid	RTeQTL
rs2255336	KLRK1	cis	lymphoblastoid	seeQTL
rs2255336	ZNF384	cis	cerebellum	SCAN
rs2255336	KLRC3	cis	parietal	SCAN
rs2255336	KLRK1	cis	parietal	SCAN
rs2255336	KLRC2	cis	cerebellum	SCAN
rs2255336	KLRC4	cis	lesional skin	skin_eQTL
rs2255336	GNB3	cis	cerebellum	SCAN
rs2255336	KLRC4///KLRK1	Cis_1M	lymphoblastoid	RTeQTL
rs2255336	RP11-277P12.20	cis	Esophagus Mucosa	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10518400-10537000	Weak transcription	Left Ventricle	heart
2	chr12:10519600-10534800	Weak transcription	Fetal Stomach	stomach
3	chr12:10519600-10547800	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:10521800-10534600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:10522400-10534000	Weak transcription	Thymus	Thymus
6	chr12:10523000-10536000	Weak transcription	Ovary	ovary
7	chr12:10525400-10547200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:10525600-10533200	Weak transcription	Fetal Intestine Large	intestine
9	chr12:10525600-10534600	Weak transcription	Pancreas	Pancrea
10	chr12:10525800-10534400	Weak transcription	Spleen	Spleen
11	chr12:10527200-10534400	Weak transcription	Brain Substantia Nigra	brain
12	chr12:10527400-10533000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:10527400-10533000	Weak transcription	Primary T cells from cord blood	blood
14	chr12:10527400-10533200	Weak transcription	Fetal Intestine Small	intestine
15	chr12:10527400-10534400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:10527600-10538600	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:10528600-10533000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:10528800-10533000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:10528800-10533000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr12:10529800-10533000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr12:10531000-10533200	Weak transcription	Hela-S3	cervix
22	chr12:10531200-10544400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr12:10531400-10533200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:10531600-10533000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr12:10531800-10533000	Weak transcription	NHEK	skin
26	chr12:10531800-10534400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:10532000-10532400	Transcr. at gene 5' and 3'	Primary T killer naive cells fromperipheralblood	blood
28	chr12:10532000-10532600	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr12:10532000-10533000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:10532000-10534600	Strong transcription	Primary B cells from cord blood	blood
31	chr12:10532200-10532400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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