Variant report

Variant	rs200486
Chromosome Location	chr6:27779506-27779507
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:43)
CpG islands
(count:0)
Chromatin interactive
region (count:41)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:43 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:27774575-27779531	GM12891	blood:	n/a	n/a
2	POLR2A	chr6:27777602-27779564	GM19099	blood:	n/a	n/a
3	POLR2A	chr6:27777500-27779550	GM12892	blood:	n/a	n/a
4	POLR2A	chr6:27774382-27779662	K562	blood:	n/a	n/a
5	POLR2A	chr6:27777524-27779571	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr6:27776232-27779525	K562	blood:	n/a	n/a
7	PML	chr6:27776216-27781822	K562	blood:	n/a	chr6:27777813-27777821
8	POLR2A	chr6:27774441-27779690	PBDE	blood:	n/a	n/a
9	POLR2A	chr6:27774370-27779564	K562	blood:	n/a	n/a
10	POLR2A	chr6:27776207-27781903	K562	blood:	n/a	n/a
11	TAF7	chr6:27776220-27782251	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr6:27777551-27779633	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr6:27774407-27779624	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:27774157-27784396	MCF-7	breast:	n/a	n/a
15	TEAD4	chr6:27776216-27781908	K562	blood:	n/a	n/a
16	HEY1	chr6:27774206-27779667	K562	blood:	n/a	n/a
17	MTA3	chr6:27777465-27779587	GM12878	blood:	n/a	n/a
18	BCLAF1	chr6:27776189-27779716	K562	blood:	n/a	chr6:27777604-27777613
19	HEY1	chr6:27777527-27779519	K562	blood:	n/a	n/a
20	POLR2A	chr6:27776241-27781173	K562	blood:	n/a	n/a
21	NFIC	chr6:27777460-27779563	GM12878	blood:	n/a	n/a
22	CHD1	chr6:27774847-27779572	GM12878	blood:	n/a	chr6:27775204-27775214 chr6:27778702-27778712
23	POLR2A	chr6:27777562-27779588	GM18505	blood:	n/a	n/a
24	TBL1XR1	chr6:27776350-27779678	K562	blood:	n/a	n/a
25	POLR2A	chr6:27779494-27779525	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr6:27777562-27779655	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr6:27774307-27779537	K562	blood:	n/a	n/a
28	POLR2A	chr6:27777351-27779656	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr6:27777425-27779515	PANC-1	pancreas:	n/a	n/a
30	POLR2A	chr6:27777593-27779506	GM12892	blood:	n/a	n/a
31	POLR2A	chr6:27774744-27780241	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr6:27776242-27782187	K562	blood:	n/a	n/a
33	POLR2A	chr6:27774387-27779524	K562	blood:	n/a	n/a
34	HEY1	chr6:27777549-27779511	HepG2	liver:	n/a	n/a
35	POLR2A	chr6:27774296-27779517	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr6:27777555-27779525	H1-hESC	embryonic stem cell:	n/a	n/a
37	ATF2	chr6:27776228-27779588	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr6:27773907-27784120	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr6:27774322-27779691	K562	blood:	n/a	n/a
40	POLR2A	chr6:27774337-27779506	GM12878	blood:	n/a	n/a
41	CHD1	chr6:27774579-27782547	H1-hESC	embryonic stem cell:	n/a	chr6:27775204-27775214 chr6:27778702-27778712
42	POLR2A	chr6:27775490-27781797	K562	blood:	n/a	n/a
43	BCLAF1	chr6:27776201-27779775	K562	blood:	n/a	chr6:27777604-27777613

No data

(count:41 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120637307..120638899-chr6:27776878..27779705,2	K562	blood:
2	chr6:26283778..26286024-chr6:27778308..27780342,2	MCF-7	breast:
3	chr6:26122455..26127911-chr6:27777953..27784057,9	MCF-7	breast:
4	chr2:38977199..38979855-chr6:27777911..27779523,2	MCF-7	breast:
5	chr5:137802010..137804655-chr6:27778426..27781380,2	K562	blood:
6	chr6:27173443..27175541-chr6:27778725..27781351,2	K562	blood:
7	chr6:27112242..27117659-chr6:27770082..27780470,17	MCF-7	breast:
8	chr20:55842417..55844076-chr6:27778109..27779862,2	MCF-7	breast:
9	chr6:27093369..27111594-chr6:27770152..27782376,64	K562	blood:
10	chr1:43432788..43434781-chr6:27778391..27780462,2	MCF-7	breast:
11	chr6:26033235..26035308-chr6:27778375..27781238,2	MCF-7	breast:
12	chr6:26021671..26023816-chr6:27777999..27780060,2	MCF-7	breast:
13	chr6:27778583..27780437-chr6:27901055..27904160,3	K562	blood:
14	chr6:27778740..27781268-chr6:30683487..30686226,2	K562	blood:
15	chr6:27098259..27104331-chr6:27773668..27779939,16	MCF-7	breast:
16	chr6:26215420..26218815-chr6:27778137..27782519,4	MCF-7	breast:
17	chr6:26270251..26272974-chr6:27776913..27779571,3	MCF-7	breast:
18	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
19	chr6:27779050..27781755-chr6:28103031..28104802,2	K562	blood:
20	chr17:57105669..57107774-chr6:27778855..27781686,2	MCF-7	breast:
21	chr1:155099451..155102336-chr6:27776687..27779634,2	MCF-7	breast:
22	chr6:27094403..27106138-chr6:27772392..27783072,46	MCF-7	breast:
23	chr6:26275391..26278113-chr6:27778905..27781292,2	MCF-7	breast:
24	chr6:26214475..26216375-chr6:27779418..27781411,2	K562	blood:
25	chr6:26025862..26028751-chr6:27778385..27781122,2	MCF-7	breast:
26	chr6:27111360..27127716-chr6:27768319..27787545,69	MCF-7	breast:
27	chr6:27775597..27780846-chr6:28300467..28304976,7	K562	blood:
28	chr17:57913518..57917266-chr6:27775743..27780414,5	MCF-7	breast:
29	chr21:40407439..40410203-chr6:27778670..27781408,2	MCF-7	breast:
30	chr6:26215396..26217408-chr6:27778332..27780053,2	MCF-7	breast:
31	chr6:26029300..26031904-chr6:27779187..27780986,2	K562	blood:
32	chr6:27518639..27521498-chr6:27778464..27780715,2	K562	blood:
33	chr11:59313285..59315331-chr6:27779398..27781335,2	K562	blood:
34	chr6:26157592..26159745-chr6:27777609..27780154,2	MCF-7	breast:
35	chr6:27127171..27129409-chr6:27778202..27780210,2	K562	blood:
36	chr6:26054474..26058085-chr6:27777303..27780745,6	MCF-7	breast:
37	chr6:27778322..27779984-chr6:28071319..28073386,2	K562	blood:
38	chr6:27777294..27779689-chr7:138144779..138146981,2	MCF-7	breast:
39	chr6:27111749..27120986-chr6:27774460..27781468,38	K562	blood:
40	chr6:26282088..26283672-chr6:27778250..27780102,2	MCF-7	breast:
41	chr6:26197916..26207803-chr6:27772547..27779655,13	K562	blood:

No data

Variant related genes	Relation type
HIST1H2BL	TF binding region
HIST1H2BM	TF binding region
ENSG00000197409	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000137337	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000198518	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000218690	Chromatin interaction
ENSG00000089157	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000122779	Chromatin interaction
ENSG00000256018	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000217275	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000158406	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000124529	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs169262	0.80[EUR][1000 genomes]
rs200502	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs200503	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs200504	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs200956	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs200969	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs200978	0.85[ASN][1000 genomes]
rs200991	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs200994	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs201000	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs201001	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs201004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs573179	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9295740	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv1017057	chr6:27745777-27789683	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	125 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs200486	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs200486	AL022393.7	cis	Muscle Skeletal	GTEx
rs200486	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27774200-27779800	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr6:27774200-27779800	Active TSS	Thymus	Thymus
3	chr6:27774200-27779800	Active TSS	A549	lung
4	chr6:27774400-27780000	Active TSS	H9 Cell Line	embryonic stem cell
5	chr6:27774400-27780000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:27774400-27780000	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr6:27774400-27780000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:27774400-27780200	Active TSS	H1 Cell Line	embryonic stem cell
9	chr6:27774400-27784000	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:27774600-27779600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:27775200-27779600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:27775400-27779800	Active TSS	Fetal Thymus	thymus
13	chr6:27776200-27780000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:27776400-27779600	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr6:27777400-27779600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:27777800-27780600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr6:27778000-27779600	Transcr. at gene 5' and 3'	K562	blood
18	chr6:27778000-27780000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:27778000-27782200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:27778200-27779600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:27778200-27779600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr6:27778200-27782400	Weak transcription	Spleen	Spleen
23	chr6:27778400-27781800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:27778400-27782400	Weak transcription	Lung	lung
25	chr6:27778400-27782400	Weak transcription	Pancreas	Pancrea
26	chr6:27778600-27779600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr6:27778600-27779600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
28	chr6:27778600-27782600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr6:27778800-27779600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr6:27778800-27779600	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr6:27778800-27779600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:27778800-27779600	Enhancers	Fetal Heart	heart
33	chr6:27778800-27781600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr6:27778800-27782000	Weak transcription	Placenta	Placenta
35	chr6:27779000-27779600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:27779000-27779600	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr6:27779000-27779600	Flanking Active TSS	Hela-S3	cervix
38	chr6:27779000-27780000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr6:27779000-27780000	Active TSS	Brain Germinal Matrix	brain
40	chr6:27779000-27780000	Flanking Active TSS	HepG2	liver
41	chr6:27779000-27780200	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr6:27779000-27780200	Enhancers	Primary B cells from peripheral blood	blood
43	chr6:27779000-27780200	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr6:27779000-27780200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr6:27779000-27780200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:27779000-27780200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:27779000-27780200	Flanking Active TSS	Dnd41	blood
48	chr6:27779000-27780600	Weak transcription	Right Atrium	heart
49	chr6:27779000-27781600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr6:27779000-27781600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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