Variant report

Variant	rs11966045
Chromosome Location	chr6:27832269-27832270
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr6:27831980-27832883	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:27831639-27835944	MCF-7	breast:	n/a	n/a
3	POLR2A	chr6:27831648-27832275	K562	blood:	n/a	n/a
4	POLR2A	chr6:27831681-27835663	MCF-7	breast:	n/a	n/a
5	YY1	chr6:27832244-27832813	GM12891	blood:	n/a	n/a
6	YY1	chr6:27832179-27832850	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:27831846-27835556	GM18526	blood:	n/a	n/a
8	CHD1	chr6:27832173-27835389	GM12878	blood:	n/a	n/a
9	POLR2A	chr6:27831541-27835704	PBDE	blood:	n/a	n/a
10	POLR2A	chr6:27831721-27832524	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:27832217-27835503	HL-60	blood:	n/a	n/a
12	PML	chr6:27831870-27835678	GM12878	blood:	n/a	n/a
13	CREB1	chr6:27832141-27833300	GM12878	blood:	n/a	chr6:27832939-27832952
14	POLR2A	chr6:27831798-27835562	GM18505	blood:	n/a	n/a
15	BCLAF1	chr6:27831818-27832455	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:27831706-27835550	GM12891	blood:	n/a	n/a
17	POLR2A	chr6:27831646-27832468	GM12891	blood:	n/a	n/a
18	POLR2A	chr6:27831868-27832372	GM15510	blood:	n/a	n/a
19	POLR2A	chr6:27831635-27832340	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr6:27831857-27835567	GM18951	blood:	n/a	n/a
21	POLR2A	chr6:27831719-27832333	GM12878	blood:	n/a	n/a
22	POLR2A	chr6:27831639-27835590	GM12878	blood:	n/a	n/a
23	POLR2A	chr6:27831891-27832289	K562	blood:	n/a	n/a
24	GATA1	chr6:27832170-27835511	PBDE	blood:	n/a	n/a
25	POLR2A	chr6:27832216-27833341	HL-60	blood:	n/a	n/a
26	POLR2A	chr6:27831698-27832533	K562	blood:	n/a	n/a
27	BCLAF1	chr6:27831843-27832478	GM12878	blood:	n/a	n/a
28	MXI1	chr6:27831650-27836500	SK-N-SH	brain:	n/a	n/a
29	RUNX3	chr6:27831792-27835617	GM12878	blood:	n/a	n/a
30	POLR2A	chr6:27831739-27835519	GM12878	blood:	n/a	n/a
31	POLR2A	chr6:27832219-27832289	MCF-7	breast:	n/a	n/a
32	EBF1	chr6:27832254-27832758	GM12878	blood:	n/a	n/a
33	MTA3	chr6:27831574-27835630	GM12878	blood:	n/a	n/a
34	RUNX3	chr6:27831634-27835715	GM12878	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27831862..27832453-chr6:27860944..27861525,2	HCT-116	colon:
2	chr6:26154866..26157028-chr6:27832028..27836151,3	MCF-7	breast:
3	chr6:27100613..27102138-chr6:27831418..27834082,2	K562	blood:
4	chr6:26215814..26218576-chr6:27831262..27835058,4	K562	blood:
5	chr6:27832024..27834412-chr6:44214386..44216392,2	MCF-7	breast:
6	chr6:27115160..27117823-chr6:27831838..27833565,2	MCF-7	breast:
7	chr17:56707936..56710461-chr6:27831380..27834313,2	MCF-7	breast:
8	chr6:27831507..27834483-chr6:28890233..28891763,2	MCF-7	breast:
9	chr6:27113113..27117592-chr6:27831181..27837403,7	MCF-7	breast:
10	chr6:27832219..27835088-chr6:28302807..28305055,2	K562	blood:

No data

Variant related genes	Relation type
HIST1H2AL	TF binding region
HIST1H2BPS2	TF binding region
ENSG00000168274	Chromatin interaction
ENSG00000096384	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000197903	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11962485	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11962868	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11963732	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966528	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966705	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11968670	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970638	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57414310	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61072813	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922530	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73384352	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73386613	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73386619	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73386634	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73386656	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73386660	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392695	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392701	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394721	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748537	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760283	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461421	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461422	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468253	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468257	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468261	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468262	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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	nsv601208	chr6:27810626-27969004	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	237 gene(s)	inside rSNPs	diseases
7	nsv965699	chr6:27831604-27833574	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	32 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27830800-27835800	Active TSS	K562	blood
2	chr6:27831200-27832800	Weak transcription	HepG2	liver
3	chr6:27831200-27835800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr6:27831200-27835800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr6:27831400-27833000	Weak transcription	Hela-S3	cervix
6	chr6:27831400-27833800	Bivalent/Poised TSS	Brain Angular Gyrus	brain
7	chr6:27831400-27834400	Active TSS	NHDF-Ad	bronchial
8	chr6:27831400-27835600	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr6:27831600-27832400	Enhancers	Stomach Mucosa	stomach
10	chr6:27831600-27832600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:27831600-27832800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:27831600-27833400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:27831600-27833400	Active TSS	Fetal Intestine Small	intestine
14	chr6:27831600-27835400	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr6:27831600-27835600	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr6:27831600-27835800	Active TSS	Fetal Kidney	kidney
17	chr6:27831800-27832400	Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr6:27831800-27832400	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr6:27831800-27832400	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr6:27831800-27832400	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
21	chr6:27831800-27832400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr6:27831800-27832400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
23	chr6:27831800-27832400	Enhancers	Spleen	Spleen
24	chr6:27831800-27832400	Flanking Active TSS	HUVEC	blood vessel
25	chr6:27831800-27832400	Flanking Active TSS	NH-A	brain
26	chr6:27831800-27832600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:27831800-27832600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr6:27831800-27832600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr6:27831800-27832600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr6:27831800-27832600	Flanking Active TSS	Fetal Muscle Trunk	muscle
31	chr6:27831800-27832600	Flanking Active TSS	Fetal Muscle Leg	muscle
32	chr6:27831800-27832600	Enhancers	Gastric	stomach
33	chr6:27831800-27832800	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr6:27831800-27832800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
35	chr6:27831800-27832800	Flanking Active TSS	Placenta	Placenta
36	chr6:27831800-27832800	Flanking Active TSS	Fetal Thymus	thymus
37	chr6:27831800-27833000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
38	chr6:27831800-27833200	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
39	chr6:27831800-27833200	Active TSS	Fetal Brain Female	brain
40	chr6:27831800-27833400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:27831800-27833400	Active TSS	Muscle Satellite Cultured Cells	--
42	chr6:27831800-27833400	Active TSS	Fetal Lung	lung
43	chr6:27831800-27833600	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr6:27831800-27833800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:27831800-27833800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
46	chr6:27831800-27834400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr6:27831800-27834400	Active TSS	Brain Substantia Nigra	brain
48	chr6:27831800-27834400	Active TSS	Fetal Intestine Large	intestine
49	chr6:27831800-27835400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr6:27831800-27835400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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