Variant report

Variant	rs3893108
Chromosome Location	chr11:64628870-64628871
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:64628787-64628918	GM12878	blood:	n/a	n/a
2	CTCF	chr11:64628787-64628916	GM12891	blood:	n/a	n/a
3	CTCF	chr11:64628800-64628950	GM12873	blood:	n/a	chr11:64628908-64628921
4	RUNX3	chr11:64628811-64629463	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:64628864-64628914	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr11:64628802-64629242	IMR90	lung:	n/a	n/a
7	CTCF	chr11:64628747-64628905	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr11:64628780-64628930	GM12864	blood:	n/a	chr11:64628908-64628921
9	CTCF	chr11:64628800-64628950	Hela-S3	cervix:	n/a	chr11:64628908-64628921
10	MTA3	chr11:64628617-64629430	GM12878	blood:	n/a	n/a
11	CTCF	chr11:64628780-64628930	WERI-Rb-1	eye:	n/a	chr11:64628908-64628921
12	CTCF	chr11:64628780-64628930	GM12874	blood:	n/a	chr11:64628908-64628921
13	CTCF	chr11:64628780-64628930	Caco-2	colon:	n/a	chr11:64628908-64628921
14	POLR2A	chr11:64628826-64629013	GM12878	blood:	n/a	n/a
15	CTCF	chr11:64628774-64628911	GM19239	blood:	n/a	n/a
16	JUND	chr11:64628824-64628961	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr11:64628748-64628931	Hela-S3	cervix:	n/a	chr11:64628908-64628921
18	SMC3	chr11:64628794-64628902	GM12878	blood:	n/a	n/a
19	CTCF	chr11:64628698-64628887	HepG2	liver:	n/a	n/a
20	CTCF	chr11:64628814-64628900	K562	blood:	n/a	n/a
21	POLR2A	chr11:64628742-64628977	K562	blood:	n/a	n/a
22	NFATC1	chr11:64628660-64629222	GM12878	blood:	n/a	n/a
23	POLR2A	chr11:64628666-64629270	GM12892	blood:	n/a	n/a
24	MAX	chr11:64628849-64629329	NB4	blood:	n/a	n/a
25	CTCF	chr11:64628755-64628921	GM12892	blood:	n/a	chr11:64628908-64628921
26	POLR2A	chr11:64615614-64641325	GM12878	blood:	n/a	n/a
27	CTCF	chr11:64628705-64628941	H1-hESC	embryonic stem cell:	n/a	chr11:64628908-64628921
28	CTCF	chr11:64628743-64628932	GM19238	blood:	n/a	chr11:64628908-64628921
29	CTCF	chr11:64628740-64628890	HEK293	kidney:	n/a	n/a
30	CTCF	chr11:64628780-64628930	GM12873	blood:	n/a	chr11:64628908-64628921
31	CTCF	chr11:64628809-64628879	GM19240	blood:	n/a	n/a
32	POLR2A	chr11:64628687-64628948	GM12878	blood:	n/a	n/a
33	POLR2A	chr11:64628668-64628999	GM12878	blood:	n/a	n/a
34	POLR2A	chr11:64628429-64635030	GM12878	blood:	n/a	n/a
35	POLR2A	chr11:64628499-64629364	GM12892	blood:	n/a	n/a
36	POLR2A	chr11:64628796-64628911	GM12878	blood:	n/a	n/a
37	RAD21	chr11:64628720-64628979	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr11:64628820-64628970	GM12878	blood:	n/a	chr11:64628908-64628921
39	CTCF	chr11:64628780-64628930	GM12875	blood:	n/a	chr11:64628908-64628921
40	POLR2A	chr11:64628444-64629321	GM12892	blood:	n/a	n/a
41	CTCF	chr11:64628860-64629010	GM12867	blood:	n/a	chr11:64628908-64628921
42	RAD21	chr11:64628556-64628994	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
EHD1	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10897533	0.99[ASN][1000 genomes]
rs1211284	0.93[ASN][1000 genomes]
rs12573	0.95[ASN][1000 genomes]
rs12801172	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17146413	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2007521	0.99[ASN][1000 genomes]
rs2077026	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3741391	0.97[ASN][1000 genomes]
rs3937000	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41381745	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4930280	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4930281	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930685	1.00[ASN][1000 genomes]
rs57851864	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs589556	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs602347	0.91[ASN][1000 genomes]
rs607569	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620066	0.99[ASN][1000 genomes]
rs621608	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs622611	0.92[ASN][1000 genomes]
rs635722	1.00[ASN][1000 genomes]
rs641623	0.92[ASN][1000 genomes]
rs649208	0.95[ASN][1000 genomes]
rs653225	0.96[ASN][1000 genomes]
rs654580	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs656982	0.89[ASN][1000 genomes]
rs7126744	1.00[ASN][1000 genomes]
rs7926812	1.00[ASN][1000 genomes]
rs7927560	0.97[ASN][1000 genomes]
rs7943238	0.94[ASN][1000 genomes]
rs7944276	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7952306	0.99[ASN][1000 genomes]
rs7952567	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
2	nsv897695	chr11:64357072-64701030	Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
3	nsv897699	chr11:64447420-64638041	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv897700	chr11:64447420-64701030	Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription 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	1071 gene(s)	inside rSNPs	diseases
5	nsv1049744	chr11:64486615-64630149	Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv897704	chr11:64584987-64701030	Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
7	nsv897705	chr11:64591679-64701030	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
8	nsv897706	chr11:64591679-64721908	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
9	nsv897707	chr11:64600002-64701030	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
10	nsv897708	chr11:64602757-64695271	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
11	nsv870106	chr11:64610698-64640067	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64612600-64639000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr11:64613000-64629800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:64613000-64630600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr11:64617600-64629600	Weak transcription	Fetal Brain Male	brain
5	chr11:64619200-64630200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr11:64619800-64632400	Genic enhancers	Primary B cells from peripheral blood	blood
7	chr11:64620800-64630200	Weak transcription	Fetal Kidney	kidney
8	chr11:64622800-64630400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr11:64623000-64630000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:64623200-64629800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:64623200-64630800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr11:64623200-64633000	Enhancers	Primary hematopoietic stem cells	blood
13	chr11:64623400-64630600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr11:64624200-64630600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr11:64624400-64629400	Strong transcription	Fetal Stomach	stomach
16	chr11:64624600-64629800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr11:64625200-64630200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr11:64625400-64629000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr11:64625400-64634200	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr11:64626400-64629000	Weak transcription	Small Intestine	intestine
21	chr11:64626400-64630000	Weak transcription	NH-A	brain
22	chr11:64626400-64644800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr11:64626600-64629000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr11:64626600-64631000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr11:64626800-64629000	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr11:64626800-64630000	Weak transcription	Fetal Heart	heart
27	chr11:64627200-64629800	Weak transcription	HUVEC	blood vessel
28	chr11:64627400-64629800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr11:64627400-64629800	Weak transcription	Brain Hippocampus Middle	brain
30	chr11:64627400-64633000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr11:64627600-64629200	Strong transcription	NHLF	lung
32	chr11:64627600-64629600	Weak transcription	Fetal Lung	lung
33	chr11:64627600-64629800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr11:64627600-64629800	Weak transcription	Brain Angular Gyrus	brain
35	chr11:64627600-64629800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr11:64627600-64630000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr11:64627600-64630200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr11:64627600-64630600	Weak transcription	Pancreas	Pancrea
39	chr11:64627600-64630600	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr11:64627600-64633200	Enhancers	Fetal Thymus	thymus
41	chr11:64627800-64629000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr11:64627800-64629600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr11:64627800-64629800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr11:64627800-64629800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr11:64627800-64629800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr11:64627800-64629800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr11:64627800-64629800	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr11:64627800-64629800	Weak transcription	Brain Anterior Caudate	brain
49	chr11:64627800-64629800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr11:64627800-64629800	Weak transcription	Brain Germinal Matrix	brain

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