Variant report

Variant	rs13212651
Chromosome Location	chr6:27806985-27806986
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:120)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:120 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr6:27805535-27806988	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:27804355-27807788	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:27804437-27807892	Hela-S3	cervix:	n/a	n/a
4	CHD1	chr6:27804111-27807828	GM12878	blood:	n/a	chr6:27805473-27805483
5	POLR2A	chr6:27804384-27808058	MCF-7	breast:	n/a	n/a
6	BCLAF1	chr6:27802551-27808286	K562	blood:	n/a	chr6:27803234-27803242
7	CTCF	chr6:27806880-27807030	BE2_C	brain:	n/a	n/a
8	POLR2A	chr6:27804577-27807240	GM12892	blood:	n/a	n/a
9	POLR2A	chr6:27804370-27807327	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:27804313-27807755	HCT-116	colon:	n/a	n/a
11	POLR2A	chr6:27803974-27807891	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr6:27804564-27807068	GM18951	blood:	n/a	n/a
13	POLR2A	chr6:27804083-27807980	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr6:27805572-27807217	A549	lung:	n/a	n/a
15	ZBTB33	chr6:27806734-27807124	A549	lung:	n/a	n/a
16	POLR2A	chr6:27804194-27807896	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr6:27804418-27807910	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:27804165-27807856	GM12878	blood:	n/a	n/a
19	HEY1	chr6:27804138-27807845	HepG2	liver:	n/a	n/a
20	RUNX3	chr6:27806737-27807109	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:27804639-27806993	GM18526	blood:	n/a	n/a
22	POLR2A	chr6:27804538-27807935	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr6:27804233-27807853	GM12891	blood:	n/a	n/a
24	POLR2A	chr6:27804505-27807298	GM12878	blood:	n/a	n/a
25	POLR2A	chr6:27796592-27807059	K562	blood:	n/a	n/a
26	POLR2A	chr6:27804330-27807822	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr6:27804449-27807764	GM12891	blood:	n/a	n/a
28	POLR2A	chr6:27803885-27807892	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr6:27805572-27807311	MCF-7	breast:	n/a	n/a
30	USF2	chr6:27804588-27807128	Hela-S3	cervix:	n/a	n/a
31	PML	chr6:27803632-27808099	K562	blood:	n/a	n/a
32	POLR2A	chr6:27804464-27807893	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr6:27804478-27807274	HL-60	blood:	n/a	n/a
34	POLR2A	chr6:27803841-27808080	HepG2	liver:	n/a	n/a
35	SMC3	chr6:27806874-27807071	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr6:27804411-27807971	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr6:27803911-27807364	K562	blood:	n/a	n/a
38	POLR2A	chr6:27804522-27807720	GM18505	blood:	n/a	n/a
39	POLR2A	chr6:27804466-27807738	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr6:27804194-27807901	PFSK-1	brain:	n/a	n/a
41	POLR2A	chr6:27804391-27807977	SK-N-MC	brain:	n/a	n/a
42	POLR2A	chr6:27804484-27807934	HUVEC	blood vessel:	n/a	n/a
43	NFIC	chr6:27804196-27807753	GM12878	blood:	n/a	n/a
44	SIN3AK20	chr6:27806721-27807051	K562	blood:	n/a	n/a
45	MAX	chr6:27804641-27807011	K562	blood:	n/a	n/a
46	POLR2A	chr6:27806971-27807310	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr6:27805559-27807277	MCF-7	breast:	n/a	n/a
48	MYBL2	chr6:27804273-27808088	HepG2	liver:	n/a	n/a
49	HEY1	chr6:27803986-27807970	K562	blood:	n/a	n/a
50	POLR2A	chr6:27804556-27807858	HUVEC	blood vessel:	n/a	n/a

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26214556..26218152-chr6:27805510..27808232,3	K562	blood:
2	chr6:26124217..26124895-chr6:27806411..27807255,2	Hela-S3	cervix:
3	chr6:27805809..27807448-chr6:28184413..28187037,2	MCF-7	breast:
4	chr6:26216271..26217870-chr6:27804676..27807375,2	MCF-7	breast:
5	chr1:119682955..119683529-chr6:27806277..27807071,2	Hela-S3	cervix:
6	chr6:27098188..27105257-chr6:27800590..27808222,20	K562	blood:
7	chr6:26026035..26027624-chr6:27806330..27807928,2	K562	blood:
8	chr6:26102660..26104205-chr6:27804912..27807560,2	MCF-7	breast:
9	chr6:27805383..27807774-chr6:28104061..28105899,2	MCF-7	breast:
10	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
11	chr6:26024775..26027574-chr6:27806170..27808884,2	MCF-7	breast:
12	chr6:26029609..26032521-chr6:27805360..27808240,3	MCF-7	breast:
13	chr1:173792439..173793277-chr6:27806309..27807278,2	Hela-S3	cervix:
14	chr6:27805460..27807795-chr6:28047138..28049507,2	MCF-7	breast:
15	chr6:26020896..26022698-chr6:27805218..27807913,2	MCF-7	breast:
16	chr6:26156285..26158369-chr6:27805497..27807966,2	K562	blood:
17	chr3:49131901..49134800-chr6:27804680..27807035,2	K562	blood:
18	chr6:27805731..27807802-chr6:27860576..27861707,5	Hela-S3	cervix:
19	chr6:27111071..27119431-chr6:27801399..27810552,22	K562	blood:
20	chr6:26154851..26161490-chr6:27803982..27809302,10	MCF-7	breast:
21	chr6:26248548..26251573-chr6:27804548..27807242,3	MCF-7	breast:
22	chr6:26251588..26253194-chr6:27805528..27807609,2	MCF-7	breast:
23	chr6:26054979..26056713-chr6:27806110..27807728,2	MCF-7	breast:
24	chr6:26204681..26207115-chr6:27805289..27807793,3	MCF-7	breast:

No data

Variant related genes	Relation type
HIST1H2AK	TF binding region
ENSG00000256316	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000272009	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000197061	Chromatin interaction
ENSG00000231365	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000198518	Chromatin interaction
ENSG00000120334	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000197279	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000116874	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000197459	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000172053	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000261839	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs13192965	0.83[EUR][1000 genomes]
rs13193295	0.89[EUR][1000 genomes]
rs13193480	0.89[EUR][1000 genomes]
rs13193542	0.89[EUR][1000 genomes]
rs13194781	1.00[CEU][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13195728	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13199649	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs13199772	1.00[CEU][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13199906	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13200214	0.82[EUR][1000 genomes]
rs13202291	0.87[EUR][1000 genomes]
rs13202295	0.89[EUR][1000 genomes]
rs13210634	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs13212318	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13215275	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs13216117	0.96[EUR][1000 genomes]
rs13217620	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs13218875	1.00[CEU][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs149943	0.83[CEU][hapmap]
rs149990	0.83[CEU][hapmap]
rs175597	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs17693963	1.00[CEU][hapmap]
rs17695758	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17749927	0.83[EUR][1000 genomes]
rs17750747	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17751184	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17763089	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs188015	0.81[EUR][1000 genomes]
rs200481	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs200482	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs200483	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs200484	0.91[CEU][hapmap]
rs200485	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs200489	0.86[EUR][1000 genomes]
rs200490	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs200493	0.82[EUR][1000 genomes]
rs200497	0.85[EUR][1000 genomes]
rs200501	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs200948	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs200949	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs200950	0.90[EUR][1000 genomes]
rs200952	0.90[EUR][1000 genomes]
rs200953	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs200954	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs200977	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs200981	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs200983	0.88[EUR][1000 genomes]
rs200989	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs200990	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs200992	0.83[EUR][1000 genomes]
rs200995	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs200996	0.88[EUR][1000 genomes]
rs201002	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs2747054	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs28360499	0.95[EUR][1000 genomes]
rs34064842	0.85[EUR][1000 genomes]
rs34194357	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34295134	0.88[EUR][1000 genomes]
rs34409918	0.85[EUR][1000 genomes]
rs34432857	0.85[EUR][1000 genomes]
rs34706883	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34718920	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34788973	0.96[EUR][1000 genomes]
rs35037868	0.89[EUR][1000 genomes]
rs35501037	0.89[EUR][1000 genomes]
rs35715914	0.83[EUR][1000 genomes]
rs35819751	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36101351	0.96[EUR][1000 genomes]
rs36116761	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs370155	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs390764	0.86[EUR][1000 genomes]
rs401754	0.86[EUR][1000 genomes]
rs401763	0.91[CEU][hapmap]
rs425335	1.00[CEU][hapmap]
rs45509595	1.00[EUR][1000 genomes]
rs483143	0.88[EUR][1000 genomes]
rs493161	0.90[EUR][1000 genomes]
rs557042	0.90[EUR][1000 genomes]
rs56405707	0.83[EUR][1000 genomes]
rs61742093	0.96[EUR][1000 genomes]
rs66868086	1.00[EUR][1000 genomes]
rs67040724	0.96[EUR][1000 genomes]
rs67101035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67652222	0.81[EUR][1000 genomes]
rs71537572	0.89[EUR][1000 genomes]
rs71559038	0.82[EUR][1000 genomes]
rs71559050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71559051	0.81[AMR][1000 genomes]
rs71559054	0.96[EUR][1000 genomes]
rs72845070	0.83[EUR][1000 genomes]
rs72847313	0.89[EUR][1000 genomes]
rs9368531	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
3	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
4	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
5	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
6	nsv969367	chr6:27805874-27807512	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	64 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13212651	BTN3A2	trans	lymphoblastoid	seeQTL
rs13212651	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs13212651	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs13212651	LOC100270746	cis	lymphoblastoid	seeQTL
rs13212651	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs13212651	AL022393.7	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27802800-27808200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:27803200-27807400	Active TSS	K562	blood
3	chr6:27803200-27807600	Active TSS	Fetal Thymus	thymus
4	chr6:27803200-27808200	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:27803400-27808000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:27803400-27808400	Active TSS	GM12878-XiMat	blood
7	chr6:27803800-27807800	Active TSS	Fetal Intestine Large	intestine
8	chr6:27803800-27808200	Active TSS	Thymus	Thymus
9	chr6:27804000-27807600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:27804000-27807800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:27804000-27808000	Active TSS	H1 Cell Line	embryonic stem cell
12	chr6:27804000-27808000	Active TSS	HSMMtube	muscle
13	chr6:27804000-27808200	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr6:27804200-27807200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:27804200-27807400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:27804200-27807400	Bivalent/Poised TSS	Brain Substantia Nigra	brain
17	chr6:27804200-27807600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:27804200-27807600	Active TSS	Aorta	Aorta
19	chr6:27804200-27807800	Active TSS	H9 Cell Line	embryonic stem cell
20	chr6:27804200-27807800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
21	chr6:27804200-27807800	Active TSS	Psoas Muscle	Psoas
22	chr6:27804200-27808000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:27804200-27808000	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr6:27804200-27808000	Active TSS	A549	lung
25	chr6:27804400-27807000	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr6:27804400-27807400	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr6:27804400-27807400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:27804400-27807400	Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr6:27804400-27807400	Active TSS	Colon Smooth Muscle	Colon
30	chr6:27804400-27807600	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr6:27804400-27807600	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr6:27804400-27807600	Active TSS	Colonic Mucosa	Colon
33	chr6:27804400-27807600	Active TSS	Fetal Intestine Small	intestine
34	chr6:27804400-27807600	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr6:27804400-27807800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr6:27804400-27807800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr6:27804400-27807800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr6:27804400-27807800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:27804400-27807800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:27804400-27807800	Active TSS	Fetal Heart	heart
41	chr6:27804400-27807800	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr6:27804400-27807800	Active TSS	NHDF-Ad	bronchial
43	chr6:27804400-27807800	Active TSS	NHLF	lung
44	chr6:27804400-27808000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr6:27804400-27808000	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr6:27804400-27808000	Active TSS	Hela-S3	cervix
47	chr6:27804400-27808200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr6:27804600-27807000	Active TSS	Gastric	stomach
49	chr6:27804600-27807200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:27804600-27807400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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