Variant report

Variant	rs11235937
Chromosome Location	chr11:73586529-73586530
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:73586228-73586833	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr11:73586246-73588801	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr11:73585876-73588793	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr11:73585989-73587043	HepG2	liver:	n/a	n/a
5	HEY1	chr11:73586204-73586658	K562	blood:	n/a	chr11:73586289-73586298
6	POLR2A	chr11:73586074-73586974	PANC-1	pancreas:	n/a	n/a
7	CHD1	chr11:73586412-73588475	H1-hESC	embryonic stem cell:	n/a	n/a
8	MYC	chr11:73586428-73588664	A549	lung:	n/a	chr11:73587946-73587954
9	POLR2A	chr11:73586022-73587172	GM12891	blood:	n/a	n/a
10	WRNIP1	chr11:73586465-73587264	GM12878	blood:	n/a	n/a
11	POLR2A	chr11:73585952-73586718	HepG2	liver:	n/a	n/a
12	POLR2A	chr11:73585707-73586807	K562	blood:	n/a	n/a
13	POLR2A	chr11:73585758-73588498	GM12892	blood:	n/a	n/a
14	HEY1	chr11:73586115-73586576	HepG2	liver:	n/a	chr11:73586289-73586298
15	POLR2A	chr11:73585961-73586670	GM12891	blood:	n/a	n/a
16	POLR2A	chr11:73585925-73586672	H1-hESC	embryonic stem cell:	n/a	n/a
17	USF2	chr11:73586394-73586704	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr11:73586039-73588558	HepG2	liver:	n/a	n/a
19	POLR2A	chr11:73586513-73586667	MCF-7	breast:	n/a	n/a
20	POLR2A	chr11:73585923-73588429	GM12878	blood:	n/a	n/a
21	POLR2A	chr11:73586221-73587110	GM12892	blood:	n/a	n/a
22	POLR2A	chr11:73585928-73588368	GM12878	blood:	n/a	n/a
23	POLR2A	chr11:73585925-73586670	GM12892	blood:	n/a	n/a
24	POLR2A	chr11:73585872-73586699	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr11:73586144-73588619	GM12891	blood:	n/a	n/a
26	POLR2A	chr11:73586136-73587206	GM12892	blood:	n/a	n/a
27	POLR2A	chr11:73586283-73588352	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr11:73584983-73586623	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:73586190..73586861-chr5:179247491..179248383,2	MCF-7	breast:
2	chr11:73584965..73587189-chr11:73691735..73694698,2	K562	blood:
3	chr11:73586195..73589455-chr11:73595184..73599458,5	K562	blood:
4	chr11:73497934..73501442-chr11:73586433..73589232,4	K562	blood:
5	chr11:73561396..73563190-chr11:73586295..73588149,3	MCF-7	breast:
6	chr11:73497415..73503223-chr11:73585602..73589591,8	K562	blood:
7	chr11:73585766..73589510-chr11:73599101..73602813,5	MCF-7	breast:

No data

Variant related genes	Relation type
PAAF1	TF binding region
COA4	TF binding region
ENSG00000161011	Chromatin interaction
ENSG00000175567	Chromatin interaction
ENSG00000256681	Chromatin interaction
ENSG00000175575	Chromatin interaction
ENSG00000175581	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10501412	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[ASN][1000 genomes]
rs10898947	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs10898948	0.81[TSI][hapmap]
rs10898949	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs10898950	0.83[TSI][hapmap]
rs11235851	0.92[CHB][hapmap]
rs11235907	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs11235908	0.86[CHB][hapmap]
rs11235922	1.00[CHB][hapmap]
rs11235925	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[ASN][1000 genomes]
rs11235927	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs11235931	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs11235933	0.92[CHB][hapmap];0.82[CHD][hapmap];0.85[ASN][1000 genomes]
rs11235934	0.85[ASN][1000 genomes]
rs11235939	0.85[ASN][1000 genomes]
rs11235947	0.82[ASN][1000 genomes]
rs12365080	1.00[CHB][hapmap]
rs12420099	0.85[ASN][1000 genomes]
rs12420751	0.85[ASN][1000 genomes]
rs12421077	0.83[ASN][1000 genomes]
rs12421900	0.82[ASN][1000 genomes]
rs17132369	0.86[CHB][hapmap]
rs17132397	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs17132403	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs17132411	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs17132419	0.86[YRI][hapmap]
rs1814547	0.82[ASN][1000 genomes]
rs1869433	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs2067912	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs3741137	0.85[ASN][1000 genomes]
rs4537782	0.83[ASN][1000 genomes]
rs4944034	0.86[CHB][hapmap]
rs4944868	0.82[ASN][1000 genomes]
rs4944869	0.85[ASN][1000 genomes]
rs7105309	0.83[CHD][hapmap];0.81[GIH][hapmap]
rs7119528	0.86[CHB][hapmap]
rs71464090	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72982926	0.85[ASN][1000 genomes]
rs72982937	0.85[ASN][1000 genomes]
rs7926479	0.86[YRI][hapmap]
rs7939193	0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv530641	chr11:73358393-73638725	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv1038105	chr11:73552023-73673836	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1035977	chr11:73581224-73617653	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11235937	PAAF1	cis	lymphoblastoid	seeQTL
rs11235937	FAM86C	cis	parietal	SCAN
rs11235937	MRPL48	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73580200-73586600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr11:73580800-73586600	Weak transcription	Stomach Mucosa	stomach
3	chr11:73584400-73586800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:73584400-73586800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr11:73584400-73587200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr11:73584400-73587200	Weak transcription	Aorta	Aorta
7	chr11:73585000-73586600	Genic enhancers	Fetal Muscle Leg	muscle
8	chr11:73585000-73586800	Weak transcription	Left Ventricle	heart
9	chr11:73585000-73587200	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr11:73585200-73587000	Weak transcription	Lung	lung
11	chr11:73585400-73586600	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr11:73585400-73586800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:73585600-73586800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr11:73585800-73586600	Genic enhancers	Primary B cells from peripheral blood	blood
15	chr11:73585800-73586600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr11:73585800-73586800	Genic enhancers	Primary T cells fromperipheralblood	blood
17	chr11:73585800-73586800	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr11:73585800-73586800	Enhancers	Placenta	Placenta
19	chr11:73585800-73587000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr11:73585800-73587400	Enhancers	Spleen	Spleen
21	chr11:73586000-73586600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
22	chr11:73586000-73586600	Genic enhancers	Brain Angular Gyrus	brain
23	chr11:73586000-73586600	Genic enhancers	Fetal Brain Female	brain
24	chr11:73586000-73586600	Genic enhancers	Fetal Thymus	thymus
25	chr11:73586000-73586600	Enhancers	Ovary	ovary
26	chr11:73586000-73586600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
27	chr11:73586000-73586600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
28	chr11:73586000-73586800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:73586000-73586800	Enhancers	Brain Cingulate Gyrus	brain
30	chr11:73586000-73586800	Enhancers	Gastric	stomach
31	chr11:73586000-73587000	Enhancers	Pancreas	Pancrea
32	chr11:73586000-73587000	Enhancers	Right Atrium	heart
33	chr11:73586000-73587000	Transcr. at gene 5' and 3'	Dnd41	blood
34	chr11:73586000-73587000	Transcr. at gene 5' and 3'	K562	blood
35	chr11:73586200-73586600	Genic enhancers	H9 Cell Line	embryonic stem cell
36	chr11:73586200-73586600	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
37	chr11:73586200-73586600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr11:73586200-73586600	Genic enhancers	Primary T cells from cord blood	blood
39	chr11:73586200-73586600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
40	chr11:73586200-73586600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr11:73586200-73586600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr11:73586200-73586600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:73586200-73586600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
44	chr11:73586200-73586600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr11:73586200-73586600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr11:73586200-73586600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr11:73586200-73586600	Genic enhancers	Brain Germinal Matrix	brain
48	chr11:73586200-73586600	Genic enhancers	Brain Hippocampus Middle	brain
49	chr11:73586200-73586600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
50	chr11:73586200-73586600	Transcr. at gene 5' and 3'	A549	lung

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