Variant report

Variant	rs2617172
Chromosome Location	chr12:10562486-10562487
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	chr12:10560564-10566250	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
KLRC4	TF binding region
KLRC4-KLRK1	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12318583	0.86[ASN][1000 genomes]
rs1382264	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1382265	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1478309	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1478310	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1600127	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17549004	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1841958	0.84[ASN][1000 genomes]
rs2045876	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2126888	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2126889	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2246809	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255336	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2255353	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2255364	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2294147	0.81[ASN][1000 genomes]
rs2417734	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2617151	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2617152	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2617156	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2617157	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2617169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2733840	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2733845	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2733847	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2733848	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2733853	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2734561	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2734565	0.84[ASN][1000 genomes]
rs2927561	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4764430	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6488285	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7307721	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7310643	0.84[EUR][1000 genomes]
rs7957681	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7958658	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7964772	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	esv1809664	chr12:10551852-10598784	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv606	chr12:10552632-10612899	Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	nsv898767	chr12:10553930-10622047	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
20	nsv973196	chr12:10559010-10573933	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
21	nsv983434	chr12:10559010-10600415	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
22	nsv557459	chr12:10560591-10729821	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
23	nsv521062	chr12:10560957-10604945	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2617172	KLRK1	Cis_1M	lymphoblastoid	RTeQTL
rs2617172	KLRC4///KLRK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10548600-10564000	Weak transcription	Brain Angular Gyrus	brain
2	chr12:10550800-10564000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:10559800-10563800	Weak transcription	Primary B cells from cord blood	blood
4	chr12:10559800-10564000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:10562200-10563000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:10562200-10563600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:10562200-10563800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr12:10562200-10563800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr12:10562200-10564000	Weak transcription	K562	blood
10	chr12:10562200-10566600	Weak transcription	Hela-S3	cervix
11	chr12:10562200-10572800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:10562400-10563800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:10562400-10563800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:10562400-10563800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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