Variant report

Variant	rs2066496
Chromosome Location	chr11:67160961-67160962
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:67160849-67161348	K562	blood:	n/a	n/a
2	POLR2A	chr11:67160761-67161344	K562	blood:	n/a	n/a
3	POLR2A	chr11:67160882-67161191	HepG2	liver:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:67160326..67163213-chr11:67229848..67232719,2	MCF-7	breast:
2	chr11:67157917..67161280-chr11:67271512..67274163,3	MCF-7	breast:
3	chr11:67159421..67161559-chr11:67272153..67274079,2	K562	blood:
4	chr11:67159952..67162907-chr11:67231636..67233328,2	K562	blood:
5	chr11:67033658..67035636-chr11:67159466..67162456,3	MCF-7	breast:
6	chr11:67138430..67143112-chr11:67157518..67161987,7	K562	blood:
7	chr11:67158791..67161769-chr11:67261033..67263210,2	K562	blood:
8	chr11:67070042..67072610-chr11:67159168..67161895,3	MCF-7	breast:
9	chr11:67116454..67122701-chr11:67156914..67162562,7	K562	blood:
10	chr11:67019300..67021347-chr11:67159445..67161762,2	K562	blood:
11	chr11:67054211..67056226-chr11:67160780..67163309,2	MCF-7	breast:
12	chr11:67156232..67161608-chr11:67271298..67276147,11	MCF-7	breast:
13	chr11:67156700..67160978-chr11:67234255..67237148,8	MCF-7	breast:

No data

Variant related genes	Relation type
RAD9A	TF binding region
ENSG00000172932	Chromatin interaction
ENSG00000256514	Chromatin interaction
ENSG00000110697	Chromatin interaction
ENSG00000173020	Chromatin interaction
ENSG00000172663	Chromatin interaction
ENSG00000175505	Chromatin interaction
ENSG00000173120	Chromatin interaction
ENSG00000175482	Chromatin interaction
ENSG00000167797	Chromatin interaction
ENSG00000172830	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10896167	0.88[CEU][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap]
rs10896172	0.83[CHB][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap]
rs1115051	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11227756	0.84[CHD][hapmap]
rs11227788	0.85[ASN][1000 genomes]
rs12276833	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12288107	0.80[CEU][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap]
rs12290164	0.80[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs12788752	0.84[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap]
rs12805811	0.86[MEX][hapmap]
rs1558256	0.80[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.85[ASN][1000 genomes]
rs1558257	0.83[CHB][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap]
rs1638566	0.88[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs1638567	0.88[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs1638571	0.88[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1638574	0.80[ASN][1000 genomes]
rs1638586	1.00[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs1790733	0.80[CEU][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap]
rs1790740	0.88[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs1790747	0.80[CEU][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap]
rs2071007	0.84[CHD][hapmap]
rs2256154	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs2286620	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2514256	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2514258	0.82[ASN][1000 genomes]
rs34087937	0.86[MEX][hapmap]
rs35821109	0.86[MEX][hapmap]
rs3758943	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs3781941	0.88[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs3781942	0.88[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs3781943	0.88[CEU][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap]
rs3909168	0.81[ASN][1000 genomes]
rs3927807	0.88[CEU][hapmap]
rs4255546	0.88[CEU][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap]
rs4542419	0.84[CHD][hapmap]
rs4930192	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs4930197	0.88[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs4930418	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs674499	0.83[GIH][hapmap]
rs7106352	0.80[ASN][1000 genomes]
rs7480390	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs872109	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs872110	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv933183	chr11:67008447-67160993	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv897796	chr11:67021518-67186000	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv897797	chr11:67023040-67293234	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
5	nsv1043037	chr11:67027193-67357425	Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv468603	chr11:67033076-67164495	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
7	nsv555253	chr11:67033076-67164495	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
8	nsv897801	chr11:67033076-67432479	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
9	nsv1047890	chr11:67058231-67184436	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
10	nsv1048230	chr11:67058231-67252397	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	146 gene(s)	inside rSNPs	diseases
11	nsv897804	chr11:67090571-67224278	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
12	nsv1039205	chr11:67135246-67252397	Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
13	esv1818769	chr11:67138811-67300457	Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
14	esv1798859	chr11:67139954-67272983	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
15	nsv897805	chr11:67155210-67283891	ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
16	nsv897806	chr11:67155210-67294308	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
17	nsv897807	chr11:67155210-67414492	Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
18	nsv897808	chr11:67155210-67419855	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
19	nsv897809	chr11:67156875-67276235	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2066496	RPS6KB2	cis	multi-tissue	Pritchard
rs2066496	TBC1D10C	cis	multi-tissue	Pritchard
rs2066496	RPS6KB2	cis	Lymphoblastoid	GTEx
rs2066496	RPS6KB2	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67160000-67161000	Enhancers	Sigmoid Colon	Sigmoid Colon
2	chr11:67160000-67162000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr11:67160000-67163600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:67160000-67165000	Weak transcription	Aorta	Aorta
5	chr11:67160200-67161000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:67160200-67161000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr11:67160200-67162000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr11:67160200-67163000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:67160200-67165000	Weak transcription	Small Intestine	intestine
10	chr11:67160200-67166200	Weak transcription	Fetal Kidney	kidney
11	chr11:67160200-67167000	Weak transcription	Psoas Muscle	Psoas
12	chr11:67160400-67161000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:67160400-67161000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:67160400-67161000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr11:67160400-67161000	Enhancers	Primary T cells from cord blood	blood
16	chr11:67160400-67161000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr11:67160400-67161000	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr11:67160400-67161000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr11:67160400-67161000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr11:67160400-67161000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr11:67160400-67161000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr11:67160400-67161000	Genic enhancers	Brain Germinal Matrix	brain
23	chr11:67160400-67161000	Enhancers	Fetal Heart	heart
24	chr11:67160400-67161000	Weak transcription	Lung	lung
25	chr11:67160400-67161000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr11:67160400-67161000	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr11:67160400-67161000	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr11:67160400-67161200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr11:67160400-67161200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr11:67160400-67161200	Enhancers	Primary B cells from cord blood	blood
31	chr11:67160400-67161200	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr11:67160400-67161200	Genic enhancers	Fetal Brain Female	brain
33	chr11:67160400-67161200	Enhancers	Stomach Smooth Muscle	stomach
34	chr11:67160400-67161400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr11:67160400-67161400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr11:67160400-67161400	Weak transcription	Placenta	Placenta
37	chr11:67160400-67161400	Weak transcription	NHEK	skin
38	chr11:67160400-67161600	Genic enhancers	Primary B cells from peripheral blood	blood
39	chr11:67160400-67161600	Weak transcription	Brain Substantia Nigra	brain
40	chr11:67160400-67161600	Genic enhancers	Right Ventricle	heart
41	chr11:67160400-67161800	Enhancers	Primary T cells fromperipheralblood	blood
42	chr11:67160400-67161800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr11:67160400-67161800	Genic enhancers	Fetal Muscle Leg	muscle
44	chr11:67160400-67161800	Genic enhancers	Fetal Thymus	thymus
45	chr11:67160400-67162000	Strong transcription	NHLF	lung
46	chr11:67160400-67162600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr11:67160400-67162800	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr11:67160400-67162800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr11:67160400-67162800	Weak transcription	Osteobl	bone
50	chr11:67160400-67163000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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