Variant report

Variant	rs1841958
Chromosome Location	chr12:10562089-10562090
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:10561934-10562385	Hela-S3	cervix:	n/a	n/a
2	SMC3	chr12:10562041-10562349	Hela-S3	cervix:	n/a	n/a
3	TEAD4	chr12:10561954-10562323	K562	blood:	n/a	n/a
4	YY1	chr12:10562045-10562372	HCT-116	colon:	n/a	n/a
5	STAT3	chr12:10562086-10562296	Hela-S3	cervix:	n/a	n/a
6	IRF3	chr12:10562038-10562427	Hela-S3	cervix:	n/a	n/a
7	SP1	chr12:10561836-10562459	HCT-116	colon:	n/a	n/a
8	CEBPB	chr12:10562055-10562317	Hela-S3	cervix:	n/a	n/a
9	MXI1	chr12:10562084-10562381	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr12:10562040-10562330	Hela-S3	cervix:	n/a	n/a
11	STAT1	chr12:10562050-10562418	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr12:10562020-10562332	HCT-116	colon:	n/a	n/a
13	EP300	chr12:10562057-10562257	Hela-S3	cervix:	n/a	n/a
14	BRCA1	chr12:10562044-10562186	Hela-S3	cervix:	n/a	n/a
15	TBP	chr12:10562046-10562304	Hela-S3	cervix:	n/a	n/a
16	TAL1	chr12:10562038-10562379	K562	blood:	n/a	n/a
17	CHD2	chr12:10562076-10562277	Hela-S3	cervix:	n/a	n/a
18	MYC	chr12:10562084-10562315	NB4	blood:	n/a	n/a
19	RFX5	chr12:10562056-10562425	Hela-S3	cervix:	n/a	n/a
20	GTF2F1	chr12:10562044-10562327	Hela-S3	cervix:	n/a	n/a
21	TCF7L2	chr12:10561873-10562372	HCT-116	colon:	n/a	n/a
22	ARID3A	chr12:10562084-10562332	K562	blood:	n/a	n/a
23	POLR2A	chr12:10561924-10562243	Hela-S3	cervix:	n/a	n/a
24	TAF1	chr12:10562047-10562268	Hela-S3	cervix:	n/a	n/a
25	CTCF	chr12:10562065-10562123	Spleen_OC	spleen:	n/a	n/a
26	RAD21	chr12:10562062-10562333	Hela-S3	cervix:	n/a	n/a
27	MAX	chr12:10562052-10562396	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr12:10561952-10562348	Hela-S3	cervix:	n/a	n/a
29	BHLHE40	chr12:10562058-10562261	K562	blood:	n/a	n/a
30	POLR2A	chr12:10560564-10566250	Hela-S3	cervix:	n/a	n/a
31	MAFK	chr12:10562048-10562298	Hela-S3	cervix:	n/a	n/a

No data

Variant related genes	Relation type
KLRC4-KLRK1	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1049172	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs1049174	0.95[CEU][hapmap]
rs11053801	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap]
rs11053802	1.00[CEU][hapmap]
rs11053803	0.81[CEU][hapmap]
rs11838084	0.83[ASN][1000 genomes]
rs12824474	0.80[CHB][hapmap]
rs1351111	0.92[EUR][1000 genomes]
rs1351113	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs1382265	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs1841957	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2086098	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2086099	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2246809	0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs2255336	0.82[JPT][hapmap]
rs2255364	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2417734	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2617149	0.95[CEU][hapmap]
rs2617150	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2617151	0.82[JPT][hapmap]
rs2617152	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2617156	0.86[CHB][hapmap]
rs2617160	0.95[CEU][hapmap]
rs2617169	0.84[ASN][1000 genomes]
rs2617170	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2617171	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2617172	0.84[ASN][1000 genomes]
rs2682472	0.80[CEU][hapmap]
rs2733847	0.86[JPT][hapmap]
rs2733851	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2733852	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2734561	0.90[YRI][hapmap];0.82[ASN][1000 genomes]
rs2734565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2927561	0.82[CHB][hapmap]
rs7975996	0.82[EUR][1000 genomes]
rs7978962	0.80[AMR][1000 genomes];0.82[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1841958	KLRC4///KLRK1	Cis_1M	lymphoblastoid	RTeQTL
rs1841958	KLRK1	cis	multi-tissue	Pritchard
rs1841958	KLRK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 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	chr12:10558200-10562200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:10558200-10562200	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:10558800-10562400	Active TSS	Primary T cells fromperipheralblood	blood
6	chr12:10559600-10562200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:10559800-10562200	Active TSS	Primary T cells from cord blood	blood
8	chr12:10559800-10562400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
9	chr12:10559800-10562400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:10559800-10563800	Weak transcription	Primary B cells from cord blood	blood
11	chr12:10559800-10564000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:10561400-10562200	Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr12:10561400-10562200	Enhancers	K562	blood
14	chr12:10561400-10562400	Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr12:10561600-10562200	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr12:10561600-10562200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr12:10561600-10562200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr12:10561600-10562200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:10561800-10562200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr12:10561800-10562200	Enhancers	Hela-S3	cervix
21	chr12:10562000-10562200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:10562000-10562200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:10562000-10562200	Flanking Active TSS	Fetal Thymus	thymus
24	chr12:10562000-10562400	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr12:10562000-10562400	Enhancers	Brain Hippocampus Middle	brain

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