Variant report

Variant	rs560603
Chromosome Location	chr11:62625911-62625912
allele	A/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	SIN3AK20	chr11:62625613-62625963	K562	blood:	n/a	n/a
2	SIN3A	chr11:62625753-62625929	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr11:62625610-62626054	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr11:62624500-62626198	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr11:62625552-62625914	K562	blood:	n/a	n/a
6	POLR2A	chr11:62625868-62625958	HepG2	liver:	n/a	n/a
7	FOXA2	chr11:62625660-62625960	HepG2	liver:	n/a	n/a
8	RCOR1	chr11:62625739-62625953	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:62565367..62576307-chr11:62617328..62626616,39	K562	blood:
2	chr11:62614063..62631836-chr11:62641578..62658963,131	K562	blood:

Variant related genes	Relation type
SNHG1	TF binding region
ENSG00000168003	Chromatin interaction
ENSG00000162231	Chromatin interaction
ENSG00000269463	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs2730030	1.00[AMR][1000 genomes]
rs2730033	1.00[AMR][1000 genomes]
rs2956139	1.00[AMR][1000 genomes]
rs481272	1.00[AMR][1000 genomes]
rs482331	1.00[AMR][1000 genomes]
rs489275	1.00[AMR][1000 genomes]
rs507101	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs519473	0.82[AFR][1000 genomes]
rs560006	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs561385	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs561520	1.00[AMR][1000 genomes]
rs56226867	1.00[AMR][1000 genomes]
rs564587	1.00[AMR][1000 genomes]
rs577071	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs595108	1.00[AMR][1000 genomes]
rs694678	1.00[AMR][1000 genomes]
rs73487819	1.00[AMR][1000 genomes]
rs73487834	0.87[AFR][1000 genomes]
rs73487878	0.82[AFR][1000 genomes]
rs73487879	0.82[AFR][1000 genomes]
rs73487880	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv532284	chr11:62220043-62630253	Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong 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	1401 gene(s)	inside rSNPs	diseases
4	nsv508636	chr11:62547114-62644458	Transcr. at gene 5' and 3' Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1195 gene(s)	inside rSNPs	diseases
5	nsv1051308	chr11:62564713-62673136	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1199 gene(s)	inside rSNPs	diseases
6	nsv541058	chr11:62564713-62673136	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1199 gene(s)	inside rSNPs	diseases
7	nsv1041770	chr11:62610353-62871767	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	263 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62620600-62626000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:62620800-62626000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:62623000-62626000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:62623000-62626400	Active TSS	H1 Cell Line	embryonic stem cell
5	chr11:62623000-62626400	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr11:62623000-62626600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:62623000-62627000	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr11:62623200-62626400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr11:62623200-62626400	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr11:62623200-62627000	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr11:62624200-62626000	Enhancers	Placenta Amnion	Placenta Amnion
12	chr11:62624200-62627000	Weak transcription	Gastric	stomach
13	chr11:62624200-62630600	Weak transcription	HSMMtube	muscle
14	chr11:62624200-62646800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr11:62624400-62626000	Enhancers	Fetal Brain Male	brain
16	chr11:62624400-62626200	Enhancers	Placenta	Placenta
17	chr11:62624400-62628400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:62624400-62629800	Weak transcription	Primary B cells from cord blood	blood
19	chr11:62624400-62629800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr11:62624400-62631200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:62624400-62638400	Weak transcription	Fetal Stomach	stomach
22	chr11:62624400-62646800	Weak transcription	Osteobl	bone
23	chr11:62624600-62626000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr11:62624600-62630000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr11:62624600-62639600	Weak transcription	Fetal Intestine Large	intestine
26	chr11:62624600-62645600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr11:62624800-62626000	Enhancers	Fetal Intestine Small	intestine
28	chr11:62625000-62626000	Flanking Active TSS	HepG2	liver
29	chr11:62625000-62626000	Flanking Active TSS	K562	blood
30	chr11:62625000-62626000	Flanking Active TSS	NHEK	skin
31	chr11:62625000-62629800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr11:62625000-62629800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr11:62625000-62646800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr11:62625200-62626000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr11:62625200-62626000	Flanking Active TSS	Fetal Brain Female	brain
36	chr11:62625200-62626000	Enhancers	NH-A	brain
37	chr11:62625200-62626200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr11:62625200-62628800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr11:62625200-62629400	Weak transcription	Pancreas	Pancrea
40	chr11:62625200-62629800	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr11:62625200-62630000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr11:62625200-62630200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr11:62625200-62630800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:62625200-62640800	Weak transcription	Fetal Muscle Leg	muscle
45	chr11:62625400-62626000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr11:62625400-62626000	Enhancers	Fetal Thymus	thymus
47	chr11:62625400-62626000	Transcr. at gene 5' and 3'	A549	lung
48	chr11:62625400-62626000	Transcr. at gene 5' and 3'	Hela-S3	cervix
49	chr11:62625400-62629800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr11:62625400-62630800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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