Variant report

Variant	rs1892940
Chromosome Location	chr11:66111251-66111252
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:66111117-66111310	HepG2	liver:	n/a	n/a
2	POLR2A	chr11:66110953-66111277	IMR90	lung:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:66108839..66110813-chr11:66110934..66112585,3	K562	blood:
2	chr11:66084372..66086380-chr11:66109864..66112582,2	MCF-7	breast:
3	chr11:66043530..66045792-chr11:66110035..66112602,2	MCF-7	breast:
4	chr11:65625352..65628744-chr11:66111177..66113723,3	K562	blood:
5	chr11:66108764..66111622-chr11:66204863..66206886,2	K562	blood:
6	chr11:66108426..66118730-chr11:66133678..66141000,25	MCF-7	breast:
7	chr11:66056831..66061115-chr11:66109718..66114909,6	MCF-7	breast:
8	chr11:66111080..66113877-chr17:56707692..56710441,2	MCF-7	breast:
9	chr11:66054162..66056937-chr11:66109546..66111530,2	K562	blood:
10	chr11:66077296..66081246-chr11:66109722..66112526,4	K562	blood:
11	chr11:66103854..66118324-chr11:66119048..66141728,55	K562	blood:
12	chr11:66079011..66083261-chr11:66109999..66114385,7	MCF-7	breast:

No data

Variant related genes	Relation type
BRMS1	TF binding region
ENSG00000255468	TF binding region
ENSG00000174669	Chromatin interaction
ENSG00000174851	Chromatin interaction
ENSG00000254452	Chromatin interaction
ENSG00000254458	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000174744	Chromatin interaction
ENSG00000174547	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000179292	Chromatin interaction
ENSG00000174807	Chromatin interaction
ENSG00000174871	Chromatin interaction
ENSG00000172732	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1039594	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1047029	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10750784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10791869	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10791872	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10791874	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10791876	0.88[EUR][1000 genomes]
rs10896111	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10896112	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896115	0.90[EUR][1000 genomes]
rs10896116	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11227465	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11601396	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11823140	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]
rs12416747	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12576299	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12577196	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12785321	0.87[EUR][1000 genomes]
rs12785651	0.83[ASW][hapmap];0.96[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap];0.87[EUR][1000 genomes]
rs12786563	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap];0.87[EUR][1000 genomes]
rs12794121	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1546358	0.89[EUR][1000 genomes]
rs1784029	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1785633	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1785639	0.84[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1892938	0.91[ASW][hapmap];0.94[LWK][hapmap];0.82[MKK][hapmap];0.84[YRI][hapmap]
rs2236679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279861	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2279862	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2282530	0.96[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs2282531	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3016767	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3177514	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34043951	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4244813	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4466842	0.88[CEU][hapmap]
rs4930177	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4930178	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4930179	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4930181	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4930360	0.86[EUR][1000 genomes]
rs4930362	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4930363	0.89[EUR][1000 genomes]
rs4930366	0.86[EUR][1000 genomes]
rs4930368	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap];0.87[EUR][1000 genomes]
rs55998145	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56123976	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56321771	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61891449	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6591213	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6591215	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6591217	0.88[EUR][1000 genomes]
rs66810040	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7104253	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7104570	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7105015	0.87[EUR][1000 genomes]
rs7105401	0.88[EUR][1000 genomes]
rs7107191	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7110944	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7117630	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7126018	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73489638	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7938676	0.86[EUR][1000 genomes]
rs7939111	0.88[EUR][1000 genomes]
rs7940980	0.86[EUR][1000 genomes]
rs905770	1.00[CEU][hapmap];0.83[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs947978	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv897782	chr11:66099222-66116911	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	esv3328878	chr11:66107076-66111474	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
10	nsv897783	chr11:66107527-66118676	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1892940	ALDH3B1	cis	parietal	SCAN
rs1892940	SLC25A45	cis	parietal	SCAN
rs1892940	RIN1	cis	Whole Blood	GTEx
rs1892940	OVOL1	cis	parietal	SCAN
rs1892940	SCYL1	cis	lymphoblastoid	seeQTL
rs1892940	CCDC87	cis	parietal	SCAN
rs1892940	RIN1	cis	multi-tissue	Pritchard
rs1892940	ASRGL1	cis	parietal	SCAN
rs1892940	SNX32	cis	parietal	SCAN
rs1892940	ESRRA	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66104600-66111600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:66105400-66111600	Weak transcription	HUVEC	blood vessel
3	chr11:66105800-66111400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr11:66106400-66111400	Weak transcription	Small Intestine	intestine
5	chr11:66109200-66111400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:66109600-66111400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr11:66109600-66111400	Weak transcription	Brain Substantia Nigra	brain
8	chr11:66109600-66111400	Weak transcription	Fetal Brain Male	brain
9	chr11:66109600-66111400	Weak transcription	Fetal Kidney	kidney
10	chr11:66109600-66111400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr11:66109600-66111600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr11:66109600-66111600	Weak transcription	HSMMtube	muscle
13	chr11:66109600-66111800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:66109600-66111800	Weak transcription	Ovary	ovary
15	chr11:66109800-66111400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr11:66109800-66111400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr11:66109800-66111800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr11:66109800-66111800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr11:66109800-66111800	Weak transcription	Aorta	Aorta
20	chr11:66109800-66111800	Weak transcription	Esophagus	oesophagus
21	chr11:66109800-66111800	Weak transcription	Left Ventricle	heart
22	chr11:66110000-66111400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr11:66110000-66111400	Weak transcription	Fetal Lung	lung
24	chr11:66110000-66111600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr11:66110000-66111800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr11:66110000-66111800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:66110200-66111800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr11:66110400-66111400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
29	chr11:66110400-66111400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr11:66110400-66111400	Weak transcription	Right Ventricle	heart
31	chr11:66110400-66111600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr11:66110400-66111600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr11:66110400-66111600	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr11:66110400-66111600	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr11:66110400-66111800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr11:66110400-66111800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr11:66110600-66111400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:66110600-66111400	Genic enhancers	Brain Anterior Caudate	brain
39	chr11:66110600-66111400	Genic enhancers	Brain Hippocampus Middle	brain
40	chr11:66110600-66111600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr11:66110600-66111600	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr11:66110600-66111600	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr11:66110600-66111800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr11:66110600-66111800	Enhancers	Pancreas	Pancrea
45	chr11:66110600-66111800	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr11:66110800-66111400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:66110800-66111400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr11:66110800-66111400	Genic enhancers	Rectal Mucosa Donor 29	rectum
49	chr11:66110800-66111400	Genic enhancers	Rectal Mucosa Donor 31	rectum
50	chr11:66110800-66111400	Genic enhancers	Skeletal Muscle Male	skeletal muscle

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