Variant report

Variant	rs620066
Chromosome Location	chr11:64632470-64632471
allele	C/G
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	STAT1	chr11:64632418-64632996	GM12878	blood:	n/a	n/a
2	EBF1	chr11:64631540-64633649	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:64629387-64634963	GM12892	blood:	n/a	n/a
4	EP300	chr11:64631945-64633856	GM12878	blood:	n/a	chr11:64632555-64632564
5	POLR2A	chr11:64630479-64633974	GM12878	blood:	n/a	n/a
6	RELA	chr11:64632004-64633707	GM19099	blood:	n/a	n/a
7	POLR2A	chr11:64631872-64633286	GM18951	blood:	n/a	n/a
8	BHLHE40	chr11:64631850-64633517	GM12878	blood:	n/a	chr11:64631859-64631875 chr11:64631867-64631883 chr11:64632021-64632037
9	POLR2A	chr11:64632378-64633261	GM12878	blood:	n/a	n/a
10	RELA	chr11:64631945-64633837	GM10847	blood:	n/a	n/a
11	MEF2A	chr11:64631977-64632632	GM12878	blood:	n/a	n/a
12	NFIC	chr11:64631704-64633987	GM12878	blood:	n/a	chr11:64631915-64631943
13	POLR2A	chr11:64630615-64634045	GM12878	blood:	n/a	n/a
14	FOXM1	chr11:64631780-64632718	GM12878	blood:	n/a	n/a
15	STAT5A	chr11:64631759-64633958	GM12878	blood:	n/a	chr11:64631964-64631976 chr11:64632355-64632367 chr11:64632408-64632420
16	EBF1	chr11:64631669-64632711	GM12878	blood:	n/a	n/a
17	POLR2A	chr11:64630368-64633794	IMR90	lung:	n/a	n/a
18	WRNIP1	chr11:64632071-64633250	GM12878	blood:	n/a	n/a
19	EP300	chr11:64631914-64633878	GM12878	blood:	n/a	chr11:64632555-64632564
20	POLR2A	chr11:64630682-64633977	GM18505	blood:	n/a	n/a
21	MAZ	chr11:64631899-64633197	GM12878	blood:	n/a	chr11:64632891-64632900
22	POLR2A	chr11:64630418-64633243	GM12878	blood:	n/a	n/a
23	IKZF1	chr11:64631963-64633888	GM12878	blood:	n/a	chr11:64632326-64632334
24	FOXM1	chr11:64631767-64632667	GM12878	blood:	n/a	n/a
25	SP1	chr11:64631751-64632631	GM12878	blood:	n/a	chr11:64632614-64632624 chr11:64632357-64632369 chr11:64632357-64632369 chr11:64631964-64631973 chr11:64632359-64632368 chr11:64632443-64632452 chr11:64632358-64632372 chr11:64632351-64632361 chr11:64632614-64632624
26	POLR2A	chr11:64631713-64633986	GM12891	blood:	n/a	n/a
27	POLR2A	chr11:64631841-64633953	GM12891	blood:	n/a	n/a
28	RUNX3	chr11:64631193-64634072	GM12878	blood:	n/a	n/a
29	TCF3	chr11:64632084-64632606	GM12878	blood:	n/a	chr11:64632467-64632481
30	CHD2	chr11:64632005-64633670	GM12878	blood:	n/a	n/a
31	STAT5A	chr11:64630839-64634016	GM12878	blood:	n/a	chr11:64631964-64631976 chr11:64632355-64632367 chr11:64632408-64632420
32	POLR2A	chr11:64629559-64634892	GM12892	blood:	n/a	n/a
33	CUX1	chr11:64631874-64632611	GM12878	blood:	n/a	n/a
34	TBP	chr11:64631957-64632760	GM12878	blood:	n/a	n/a
35	NFATC1	chr11:64631333-64633973	GM12878	blood:	n/a	n/a
36	MXI1	chr11:64631976-64632718	GM12878	blood:	n/a	n/a
37	PAX5	chr11:64631899-64632720	GM12878	blood:	n/a	n/a
38	POLR2A	chr11:64631271-64634060	GM12891	blood:	n/a	n/a
39	BCLAF1	chr11:64631620-64634035	GM12878	blood:	n/a	chr11:64632018-64632031 chr11:64631668-64631681 chr11:64633091-64633098
40	POLR2A	chr11:64631355-64634408	U87	brain:	n/a	n/a
41	BCL3	chr11:64631729-64632848	GM12878	blood:	n/a	chr11:64632018-64632031
42	RELA	chr11:64632057-64633824	GM18951	blood:	n/a	n/a
43	CREB1	chr11:64631797-64633654	GM12878	blood:	n/a	n/a
44	NFATC1	chr11:64631823-64633893	GM12878	blood:	n/a	n/a
45	POLR2A	chr11:64631437-64633176	GM19193	blood:	n/a	n/a
46	MTA3	chr11:64631211-64634036	GM12878	blood:	n/a	n/a
47	POLR2A	chr11:64632386-64633644	Raji	blood:	n/a	n/a
48	ELF1	chr11:64631276-64632530	GM12878	blood:	n/a	n/a
49	POU2F2	chr11:64632311-64633409	GM12891	blood:	n/a	n/a
50	CHD1	chr11:64631597-64633725	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	11:64538326-64543055..11:64631647-64642645	Hela-S3	cervix:
2	11:64501239-64517861..11:64631647-64642645	H1-hESC	embryonic stem cell:	embryo
3	11:64544826-64559210..11:64631647-64642645	GM12878	blood:
4	11:64523887-64530985..11:64631647-64642645	Hela-S3	cervix:
5	11:64620201-64626490..11:64631647-64642645	Hela-S3	cervix:
6	11:64415880-64426617..11:64631647-64642645	Hela-S3	cervix:
7	11:64530985-64535815..11:64631647-64642645	Hela-S3	cervix:
8	11:64610127-64612855..11:64631647-64642645	Hela-S3	cervix:

Variant related genes	Relation type
EHD1	TF binding region
ENSG00000269290	Chromatin interaction
ENSG00000168066	Chromatin interaction
ENSG00000068976	Chromatin interaction
ENSG00000269038	Chromatin interaction
ENSG00000171219	Chromatin interaction
ENSG00000110076	Chromatin interaction
ENSG00000068831	Chromatin interaction
ENSG00000110047	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10897533	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1211284	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12573	0.87[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs12801172	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs17146413	0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2007521	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2077026	0.90[ASN][1000 genomes]
rs3741391	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3893108	0.99[ASN][1000 genomes]
rs3936999	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs3937000	0.96[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs41381745	0.94[ASN][1000 genomes]
rs4930280	0.97[ASN][1000 genomes]
rs4930281	0.99[ASN][1000 genomes]
rs4930685	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57851864	0.92[ASN][1000 genomes]
rs589556	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs602347	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs607569	0.99[ASN][1000 genomes]
rs621608	0.90[ASN][1000 genomes]
rs622611	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs635722	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs641623	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs649208	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs653225	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs654580	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs656982	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7126744	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7926812	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7927560	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7943238	0.92[ASN][1000 genomes]
rs7944276	0.87[CHB][hapmap];0.96[JPT][hapmap];0.89[ASN][1000 genomes]
rs7949887	0.82[CHB][hapmap]
rs7952306	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7952567	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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	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
6	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
7	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
8	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
9	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
10	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
11	nsv360	chr11:64632395-64659636	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1003 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 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	chr11:64623200-64633000	Enhancers	Primary hematopoietic stem cells	blood
3	chr11:64625400-64634200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr11:64626400-64644800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:64627400-64633000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr11:64627600-64633200	Enhancers	Fetal Thymus	thymus
7	chr11:64627800-64633200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr11:64628400-64633200	Enhancers	Right Atrium	heart
9	chr11:64628600-64633200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr11:64628600-64633200	Enhancers	Brain Substantia Nigra	brain
11	chr11:64628600-64633400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr11:64628600-64633600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr11:64628600-64633600	Enhancers	Placenta	Placenta
14	chr11:64628800-64633000	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr11:64628800-64633400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr11:64629000-64633000	Enhancers	Small Intestine	intestine
17	chr11:64629400-64633000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:64629400-64633000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr11:64629400-64634000	Enhancers	Psoas Muscle	Psoas
20	chr11:64629600-64632600	Enhancers	Fetal Lung	lung
21	chr11:64629600-64632800	Enhancers	Fetal Brain Male	brain
22	chr11:64629600-64633000	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr11:64629600-64633800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:64629600-64638600	Enhancers	Left Ventricle	heart
25	chr11:64629800-64632600	Enhancers	Brain Anterior Caudate	brain
26	chr11:64629800-64632600	Enhancers	HSMMtube	muscle
27	chr11:64629800-64632800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr11:64629800-64633000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:64629800-64633000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr11:64629800-64633000	Enhancers	Fetal Brain Female	brain
31	chr11:64629800-64633000	Enhancers	HUVEC	blood vessel
32	chr11:64629800-64633200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr11:64629800-64633200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr11:64629800-64633200	Enhancers	Placenta Amnion	Placenta Amnion
35	chr11:64629800-64633400	Enhancers	Brain Cingulate Gyrus	brain
36	chr11:64629800-64633400	Enhancers	Lung	lung
37	chr11:64629800-64633800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:64629800-64633800	Enhancers	Brain Angular Gyrus	brain
39	chr11:64629800-64634000	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr11:64629800-64634000	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr11:64630000-64633000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr11:64630000-64633800	Enhancers	Fetal Heart	heart
43	chr11:64630000-64633800	Enhancers	Stomach Mucosa	stomach
44	chr11:64630200-64633800	Enhancers	Liver	Liver
45	chr11:64630200-64634000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:64630400-64633000	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr11:64630400-64633000	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr11:64630400-64633000	Enhancers	Ovary	ovary
49	chr11:64630400-64634600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr11:64630600-64632800	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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