Variant report

Variant	rs11759720
Chromosome Location	chr6:26250254-26250255
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:254)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:254 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr6:26249923-26250982	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:26249516-26251102	K562	blood:	n/a	n/a
3	ZNF143	chr6:26250102-26250904	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr6:26249302-26251004	GM12892	blood:	n/a	n/a
5	ZKSCAN1	chr6:26250014-26251007	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr6:26249500-26251055	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr6:26249186-26251067	GM12892	blood:	n/a	n/a
8	POLR2A	chr6:26250042-26250978	HepG2	liver:	n/a	n/a
9	POLR2A	chr6:26249878-26251006	K562	blood:	n/a	n/a
10	CBX3	chr6:26249722-26251229	K562	blood:	n/a	n/a
11	POLR2A	chr6:26249268-26250973	H1-hESC	embryonic stem cell:	n/a	n/a
12	RCOR1	chr6:26249992-26251036	Hela-S3	cervix:	n/a	n/a
13	RELA	chr6:26249775-26250981	GM18951	blood:	n/a	n/a
14	YY1	chr6:26249861-26250914	K562	blood:	n/a	chr6:26250281-26250292
15	KAP1	chr6:26249927-26251001	HEK293	kidney:	n/a	n/a
16	POU2F2	chr6:26249407-26251017	GM12878	blood:	n/a	n/a
17	REST	chr6:26250029-26250429	SK-N-SH	brain:	n/a	n/a
18	BCL3	chr6:26249846-26250915	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:26249065-26250996	H1-hESC	embryonic stem cell:	n/a	n/a
20	YY1	chr6:26249825-26250946	GM12891	blood:	n/a	chr6:26250281-26250292
21	PAX5	chr6:26249850-26250321	GM12878	blood:	n/a	n/a
22	TAF1	chr6:26249701-26250982	GM12878	blood:	n/a	n/a
23	POLR2A	chr6:26249546-26251009	GM12892	blood:	n/a	n/a
24	YY1	chr6:26249768-26250929	H1-hESC	embryonic stem cell:	n/a	chr6:26250281-26250292
25	CUX1	chr6:26249747-26250995	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:26247233-26251295	K562	blood:	n/a	n/a
27	POU2F2	chr6:26249778-26250996	GM12891	blood:	n/a	n/a
28	BCLAF1	chr6:26249443-26251061	K562	blood:	n/a	n/a
29	POLR2A	chr6:26250097-26250955	HUVEC	blood vessel:	n/a	n/a
30	HEY1	chr6:26249926-26251080	HepG2	liver:	n/a	n/a
31	NFIC	chr6:26249601-26251011	GM12878	blood:	n/a	n/a
32	YY1	chr6:26249835-26250928	GM12878	blood:	n/a	chr6:26250281-26250292
33	CEBPB	chr6:26249687-26251167	GM12878	blood:	n/a	n/a
34	ATF2	chr6:26249466-26251037	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr6:26250174-26251012	K562	blood:	n/a	n/a
36	TAF1	chr6:26249952-26250305	GM12892	blood:	n/a	n/a
37	ZNF143	chr6:26250098-26250964	GM12878	blood:	n/a	n/a
38	POLR2A	chr6:26249856-26251032	NB4	blood:	n/a	n/a
39	USF2	chr6:26249931-26250936	Hela-S3	cervix:	n/a	n/a
40	MYBL2	chr6:26250146-26251091	HepG2	liver:	n/a	n/a
41	POLR2A	chr6:26249399-26250999	GM19193	blood:	n/a	n/a
42	YY1	chr6:26250016-26250879	NT2-D1	testis:	n/a	chr6:26250281-26250292
43	ATF2	chr6:26249740-26251151	GM12878	blood:	n/a	n/a
44	ZBTB33	chr6:26250013-26250389	A549	lung:	n/a	n/a
45	PML	chr6:26249770-26251089	MCF-7	breast:	n/a	n/a
46	POLR2A	chr6:26249833-26251038	Gliobla	brain:	n/a	n/a
47	EBF1	chr6:26250247-26250274	GM12878	blood:	n/a	n/a
48	RAD21	chr6:26250133-26250725	Hela-S3	cervix:	n/a	n/a
49	MAX	chr6:26249784-26250485	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr6:26249811-26251035	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26250131..26252759-chr9:103947028..103949743,2	MCF-7	breast:
2	chr6:26248067..26250449-chr6:26519454..26521698,3	K562	blood:
3	chr4:10118476..10119161-chr6:26250194..26250980,2	NB4	blood:
4	chr19:10662829..10663726-chr6:26249782..26250694,2	NB4	blood:
5	chr6:26248591..26251636-chr6:26519454..26522320,3	K562	blood:
6	chr20:55838553..55841371-chr6:26249456..26251854,2	MCF-7	breast:
7	chr6:26249395..26251593-chr6:27113655..27116155,2	MCF-7	breast:
8	chr6:26248693..26251419-chr6:27106113..27108682,2	K562	blood:
9	chr6:26249129..26252003-chr6:27832611..27836378,6	MCF-7	breast:
10	chr6:26248548..26251573-chr6:27804548..27807242,3	MCF-7	breast:
11	chr17:59475732..59477627-chr6:26249790..26252547,2	MCF-7	breast:
12	chr6:26248843..26252508-chr6:27859565..27863258,4	K562	blood:
13	chr20:52209149..52211358-chr6:26249581..26251154,2	MCF-7	breast:
14	chr6:26249452..26251500-chr6:26536200..26539102,2	K562	blood:
15	chr6:26044049..26046588-chr6:26248373..26251129,2	MCF-7	breast:
16	chr17:56707658..56709350-chr6:26249313..26251402,2	MCF-7	breast:
17	chr6:26248241..26251766-chr6:27097726..27103043,5	MCF-7	breast:
18	chr6:26248634..26250834-chr7:1595430..1598246,2	MCF-7	breast:
19	chr3:4345142..4346811-chr6:26249362..26251344,2	MCF-7	breast:

No data

Variant related genes	Relation type
HIST1H2BH	TF binding region
HIST1H4G	TF binding region
ENSG00000121068	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000184348	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000164855	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000196532	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000184357	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000198374	Chromatin interaction
ENSG00000148123	Chromatin interaction
ENSG00000170364	Chromatin interaction
ENSG00000071127	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000199289	Chromatin interaction
ENSG00000233822	Chromatin interaction
ENSG00000182952	Chromatin interaction
ENSG00000234816	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000196331	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10484436	0.85[CHD][hapmap]
rs10946808	0.82[JPT][hapmap]
rs11751978	0.82[CHB][hapmap]
rs11752014	0.82[CHB][hapmap]
rs11753131	0.85[CHD][hapmap]
rs11753610	0.81[GIH][hapmap]
rs11755943	0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11758351	0.80[CHB][hapmap]
rs11759682	0.80[JPT][hapmap]
rs11759904	0.85[CHD][hapmap]
rs16891467	0.85[CHD][hapmap]
rs16891481	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16891523	0.82[CHB][hapmap]
rs16891525	0.82[CHB][hapmap]
rs1883214	0.82[CHB][hapmap]
rs1997768	0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2143345	0.85[CHD][hapmap]
rs2893842	0.82[JPT][hapmap]
rs2893843	0.90[JPT][hapmap]
rs3734533	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3823157	0.80[JPT][hapmap]
rs4412193	0.90[JPT][hapmap]
rs4631273	0.82[CHB][hapmap]
rs6901243	0.80[JPT][hapmap]
rs6913828	0.83[LWK][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs6914596	0.82[CHB][hapmap]
rs6930616	0.90[JPT][hapmap]
rs7755741	0.82[JPT][hapmap]
rs811041	0.82[JPT][hapmap]
rs9358913	0.82[JPT][hapmap]
rs9358918	0.90[JPT][hapmap]
rs9358926	0.90[JPT][hapmap]
rs9358927	0.90[JPT][hapmap]
rs9379842	0.82[JPT][hapmap]
rs9393691	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
8	nsv916992	chr6:25991630-26280921	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1159 gene(s)	inside rSNPs	diseases
9	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
10	nsv870314	chr6:26008435-26280807	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1151 gene(s)	inside rSNPs	diseases
11	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases
12	nsv1023979	chr6:26026870-26287399	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1113 gene(s)	inside rSNPs	diseases
13	nsv1015782	chr6:26026870-26323895	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1114 gene(s)	inside rSNPs	diseases
14	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
15	nsv482348	chr6:26082709-26261136	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	799 gene(s)	inside rSNPs	diseases
16	nsv601173	chr6:26239404-26322524	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	184 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11759720	HIST1H4F	cis	cerebellum	SCAN
rs11759720	HIST1H3F	cis	cerebellum	SCAN
rs11759720	HIST1H2AE	cis	lymphoblastoid	seeQTL
rs11759720	HIST1H3E	cis	cerebellum	SCAN
rs11759720	HIST1H2BG	cis	multi-tissue	Pritchard
rs11759720	HIST1H4F	cis	parietal	SCAN
rs11759720	HIST1H2AE	cis	multi-tissue	Pritchard
rs11759720	ZKSCAN4	cis	cerebellum	SCAN
rs11759720	HIST1H1D	cis	cerebellum	SCAN
rs11759720	HIST1H2AK	cis	parietal	SCAN
rs11759720	HIST1H3E	cis	parietal	SCAN
rs11759720	ZNF187	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26249200-26250400	Bivalent/Poised TSS	Liver	Liver
2	chr6:26249200-26250600	Active TSS	Primary T cells from cord blood	blood
3	chr6:26249200-26250800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr6:26249200-26251000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:26249200-26251000	Flanking Active TSS	Fetal Thymus	thymus
6	chr6:26249200-26251400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:26249200-26251800	Active TSS	Brain Germinal Matrix	brain
8	chr6:26249200-26254000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:26249200-26254200	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:26249200-26254600	Active TSS	H1 Cell Line	embryonic stem cell
11	chr6:26249400-26250400	Active TSS	Right Ventricle	heart
12	chr6:26249400-26250400	Flanking Active TSS	Dnd41	blood
13	chr6:26249400-26250400	Active TSS	HMEC	breast
14	chr6:26249400-26250800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:26249400-26250800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
16	chr6:26249400-26251000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:26249400-26251200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr6:26249400-26251600	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr6:26249400-26252000	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr6:26249400-26252400	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
21	chr6:26249400-26252600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr6:26249400-26253000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr6:26249400-26253200	Active TSS	Fetal Lung	lung
24	chr6:26249400-26253400	Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr6:26249400-26253400	Active TSS	K562	blood
26	chr6:26249400-26254000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:26249400-26254000	Active TSS	Fetal Kidney	kidney
28	chr6:26249400-26254200	Active TSS	H9 Cell Line	embryonic stem cell
29	chr6:26249400-26254200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:26249400-26254200	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr6:26249400-26254200	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr6:26249400-26254200	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr6:26249400-26254200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:26249600-26250400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
35	chr6:26249600-26250400	Active TSS	Fetal Muscle Trunk	muscle
36	chr6:26249600-26250400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
37	chr6:26249600-26250400	Active TSS	Osteobl	bone
38	chr6:26249600-26250600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:26249600-26250800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
40	chr6:26249600-26250800	Active TSS	Stomach Mucosa	stomach
41	chr6:26249600-26251000	Active TSS	A549	lung
42	chr6:26249600-26251000	Active TSS	HSMM	muscle
43	chr6:26249600-26251200	Flanking Active TSS	HUVEC	blood vessel
44	chr6:26249600-26251600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:26249600-26251600	Flanking Active TSS	NH-A	brain
46	chr6:26249600-26252000	Active TSS	Placenta	Placenta
47	chr6:26249600-26252400	Active TSS	Fetal Heart	heart
48	chr6:26249600-26253400	Active TSS	Fetal Brain Female	brain
49	chr6:26249600-26253600	Active TSS	Duodenum Mucosa	Duodenum
50	chr6:26249600-26253800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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