Variant report

Variant	rs11823140
Chromosome Location	chr11:66098322-66098323
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:66098087-66098881	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr11:66098179-66098994	IMR90	lung:	n/a	n/a
3	POLR2A	chr11:66098041-66098760	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr11:66097213-66100151	U87	brain:	n/a	n/a
5	POLR2A	chr11:66098066-66099515	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr11:66098158-66099002	HCT-116	colon:	n/a	n/a
7	POLR2A	chr11:66097286-66099531	U87	brain:	n/a	n/a
8	POLR2A	chr11:66098310-66098666	A549	lung:	n/a	n/a
9	POLR2A	chr11:66098173-66098908	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr11:66095435-66099531	U87	brain:	n/a	n/a
11	POLR2A	chr11:66097281-66098958	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr11:66094133-66099963	U87	brain:	n/a	n/a
13	POLR2A	chr11:66094758-66099273	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr11:66078962..66079655-chr11:66098111..66098921,2	K562	blood:
2	chr11:66076960..66082217-chr11:66092441..66098354,9	K562	blood:
3	chr11:66047213..66049788-chr11:66097470..66100241,3	K562	blood:
4	chr11:66096036..66100735-chr11:66109250..66113337,6	K562	blood:
5	chr11:66096831..66099072-chr11:66133272..66136044,2	MCF-7	breast:
6	chr11:66078330..66081708-chr11:66094461..66098902,4	MCF-7	breast:
7	chr11:65623324..65625591-chr11:66098179..66100735,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000254756	TF binding region
ENSG00000172757	Chromatin interaction
ENSG00000254458	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000174744	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1039594	0.87[EUR][1000 genomes]
rs1047029	0.88[EUR][1000 genomes]
rs10750784	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10791869	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10791872	0.86[EUR][1000 genomes]
rs10791874	0.83[EUR][1000 genomes]
rs10896111	0.96[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10896112	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10896115	0.83[EUR][1000 genomes]
rs10896116	0.82[EUR][1000 genomes]
rs11227465	0.88[EUR][1000 genomes]
rs11601396	0.90[EUR][1000 genomes]
rs12416747	0.85[EUR][1000 genomes]
rs12576299	0.86[EUR][1000 genomes]
rs12577196	0.86[EUR][1000 genomes]
rs12785651	0.92[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs12786563	0.92[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs12794121	0.88[EUR][1000 genomes]
rs1784029	0.88[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1785633	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1785639	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1892938	0.85[GIH][hapmap]
rs1892940	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2236679	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2279861	0.96[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs2279862	0.96[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs2282530	0.92[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs2282531	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3016767	0.88[EUR][1000 genomes]
rs3177514	0.88[EUR][1000 genomes]
rs4244813	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs4466842	0.83[CEU][hapmap]
rs4930177	0.88[EUR][1000 genomes]
rs4930178	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs4930179	0.82[EUR][1000 genomes]
rs4930362	0.82[EUR][1000 genomes]
rs4930368	0.92[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs55998145	0.82[EUR][1000 genomes]
rs56123976	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61891449	0.83[EUR][1000 genomes]
rs6591213	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs7104253	0.81[EUR][1000 genomes]
rs7104570	0.96[CEU][hapmap]
rs7107191	0.85[EUR][1000 genomes]
rs7110944	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7117630	0.83[EUR][1000 genomes]
rs7126018	0.87[EUR][1000 genomes]
rs73489638	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs905770	0.96[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs947978	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
4	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
5	nsv897772	chr11:66018155-66254085	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
6	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv897781	chr11:66095967-66116911	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	esv1813137	chr11:66098322-66106725	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11823140	ASRGL1	cis	parietal	SCAN
rs11823140	SCYL1	cis	lymphoblastoid	seeQTL
rs11823140	SNX32	cis	parietal	SCAN
rs11823140	SLC25A45	cis	parietal	SCAN
rs11823140	OVOL1	cis	parietal	SCAN
rs11823140	ESRRA	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66084600-66103200	Weak transcription	Small Intestine	intestine
2	chr11:66093200-66102800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:66094400-66102800	Weak transcription	Psoas Muscle	Psoas
4	chr11:66095000-66102800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr11:66095800-66100800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:66096400-66098400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:66096400-66099000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:66096400-66099000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr11:66096400-66099000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:66096400-66099000	Weak transcription	Fetal Intestine Small	intestine
11	chr11:66096400-66099000	Weak transcription	HMEC	breast
12	chr11:66096400-66099200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr11:66096400-66099200	Weak transcription	Brain Anterior Caudate	brain
14	chr11:66096400-66099200	Weak transcription	Esophagus	oesophagus
15	chr11:66096400-66099200	Weak transcription	Fetal Intestine Large	intestine
16	chr11:66096400-66099200	Weak transcription	Gastric	stomach
17	chr11:66096400-66099200	Weak transcription	Lung	lung
18	chr11:66096400-66099400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr11:66096400-66099400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr11:66096400-66099600	Weak transcription	Colon Smooth Muscle	Colon
21	chr11:66096400-66099600	Weak transcription	Ovary	ovary
22	chr11:66096400-66099600	Weak transcription	Right Ventricle	heart
23	chr11:66096400-66099600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr11:66096400-66099800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr11:66096400-66099800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr11:66096400-66099800	Weak transcription	Colonic Mucosa	Colon
27	chr11:66096400-66099800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr11:66096400-66100000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr11:66096400-66100000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr11:66096400-66100200	Weak transcription	Pancreas	Pancrea
31	chr11:66096400-66101000	Weak transcription	Brain Angular Gyrus	brain
32	chr11:66096400-66101600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr11:66096400-66102400	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr11:66096400-66102400	Weak transcription	HSMM	muscle
35	chr11:66096400-66102600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr11:66096400-66102600	Weak transcription	HSMMtube	muscle
37	chr11:66096400-66102800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:66096400-66102800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr11:66096400-66102800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr11:66096400-66102800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr11:66096400-66102800	Weak transcription	Left Ventricle	heart
42	chr11:66096400-66102800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr11:66096400-66102800	Weak transcription	Right Atrium	heart
44	chr11:66096400-66103000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr11:66096400-66103000	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr11:66096400-66104400	Weak transcription	Dnd41	blood
47	chr11:66096600-66098600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr11:66096600-66098800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:66096600-66098800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr11:66096600-66098800	Weak transcription	Primary monocytes fromperipheralblood	blood

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