Variant report

Variant	rs560006
Chromosome Location	chr11:62621309-62621310
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:100)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:100 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:62617779-62623719	A549	lung:	n/a	n/a
2	POLR2A	chr11:62620711-62621914	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr11:62617628-62624283	PANC-1	pancreas:	n/a	n/a
4	SP1	chr11:62621053-62621866	H1-hESC	embryonic stem cell:	n/a	chr11:62621832-62621839
5	TEAD4	chr11:62620829-62623927	K562	blood:	n/a	n/a
6	POLR2A	chr11:62618490-62624274	GM12878	blood:	n/a	n/a
7	POLR2A	chr11:62620494-62624294	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr11:62614241-62624321	H1-hESC	embryonic stem cell:	n/a	n/a
9	WRNIP1	chr11:62620785-62621783	GM12878	blood:	n/a	n/a
10	POLR2A	chr11:62621047-62621465	HepG2	liver:	n/a	n/a
11	POLR2A	chr11:62620277-62624182	HCT-116	colon:	n/a	n/a
12	POLR2A	chr11:62620342-62621539	GM12891	blood:	n/a	n/a
13	BCL3	chr11:62620304-62621380	A549	lung:	n/a	n/a
14	POLR2A	chr11:62620269-62624353	H1-hESC	embryonic stem cell:	n/a	n/a
15	CHD1	chr11:62620648-62624364	IMR90	lung:	n/a	chr11:62623537-62623544
16	POLR2A	chr11:62620391-62624313	HL-60	blood:	n/a	n/a
17	POLR2A	chr11:62618345-62623859	U87	brain:	n/a	n/a
18	TBL1XR1	chr11:62620476-62624009	K562	blood:	n/a	n/a
19	HCFC1	chr11:62618424-62624359	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr11:62617338-62625222	HepG2	liver:	n/a	n/a
21	POLR2A	chr11:62617697-62624345	HUVEC	blood vessel:	n/a	n/a
22	STAT5A	chr11:62620798-62624193	GM12878	blood:	n/a	chr11:62623472-62623495 chr11:62622243-62622266 chr11:62622026-62622037
23	POLR2A	chr11:62620329-62623949	GM18505	blood:	n/a	n/a
24	POLR2A	chr11:62621016-62621856	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr11:62617200-62623992	U87	brain:	n/a	n/a
26	POLR2A	chr11:62617721-62624372	GM12892	blood:	n/a	n/a
27	POLR2A	chr11:62620317-62624267	GM12891	blood:	n/a	n/a
28	MTA3	chr11:62620597-62624422	GM12878	blood:	n/a	n/a
29	CHD2	chr11:62620434-62622256	K562	blood:	n/a	n/a
30	POLR2A	chr11:62617309-62624309	MCF-7	breast:	n/a	n/a
31	POLR2A	chr11:62618403-62625433	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr11:62618403-62624340	GM12892	blood:	n/a	n/a
33	NFATC1	chr11:62620995-62622018	GM12878	blood:	n/a	n/a
34	POLR2A	chr11:62617206-62623986	U87	brain:	n/a	n/a
35	POLR2A	chr11:62617682-62625430	PFSK-1	brain:	n/a	n/a
36	POLR2A	chr11:62617826-62624166	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr11:62617579-62624226	GM12891	blood:	n/a	n/a
38	POLR2A	chr11:62617217-62624356	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr11:62618031-62624145	K562	blood:	n/a	n/a
40	PML	chr11:62620639-62624369	GM12878	blood:	n/a	chr11:62621884-62621892
41	TBL1XR1	chr11:62620725-62624211	K562	blood:	n/a	n/a
42	POLR2A	chr11:62620193-62624241	PANC-1	pancreas:	n/a	n/a
43	POLR2A	chr11:62620367-62621450	GM12891	blood:	n/a	n/a
44	POLR2A	chr11:62620276-62624387	GM12878	blood:	n/a	n/a
45	CHD1	chr11:62618861-62624465	H1-hESC	embryonic stem cell:	n/a	chr11:62623537-62623544
46	POLR2A	chr11:62620342-62624325	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr11:62620348-62624123	HL-60	blood:	n/a	n/a
48	MXI1	chr11:62620640-62624491	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr11:62620706-62621477	ECC-1	luminal epithelium:	n/a	n/a
50	POLR2A	chr11:62620282-62624248	K562	blood:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62620888..62622657-chr6:26157901..26159977,2	K562	blood:
2	chr11:62597102..62625754-chr11:62640222..62672995,305	MCF-7	breast:
3	chr11:62474385..62478486-chr11:62621122..62625313,5	MCF-7	breast:
4	chr11:62565367..62576307-chr11:62617328..62626616,39	K562	blood:
5	chr11:62393961..62397589-chr11:62620781..62622689,3	K562	blood:
6	chr11:62359506..62362353-chr11:62619695..62624770,4	K562	blood:
7	chr11:62543432..62547564-chr11:62620532..62624657,4	K562	blood:
8	chr1:28975074..28975699-chr11:62620850..62621583,2	Hela-S3	cervix:
9	chr11:62620136..62622532-chr8:103666422..103668667,2	K562	blood:
10	chr11:62518863..62523305-chr11:62619900..62623516,4	K562	blood:
11	chr11:62355177..62359057-chr11:62621096..62624754,3	K562	blood:
12	chr11:62552943..62561747-chr11:62616572..62625876,31	K562	blood:
13	chr11:62526894..62529687-chr11:62620957..62624297,6	K562	blood:
14	chr11:62614063..62631836-chr11:62641578..62658963,131	K562	blood:
15	chr11:62437710..62440274-chr11:62620647..62623771,3	MCF-7	breast:
16	chr11:62492343..62497215-chr11:62619514..62625025,15	MCF-7	breast:
17	chr11:62437470..62440242-chr11:62620623..62623649,4	K562	blood:
18	chr11:62492410..62497148-chr11:62620379..62625675,11	K562	blood:
19	chr11:62620807..62623183-chr11:67373400..67376083,2	MCF-7	breast:
20	chr11:62443904..62448212-chr11:62620464..62623638,4	K562	blood:
21	chr11:62526685..62530530-chr11:62620957..62624924,5	K562	blood:
22	chr11:62340910..62342684-chr11:62620301..62623051,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDR74-1	chr11:62621273-62621814	ENSG00000255717

No data

Variant related genes	Relation type
SNHG1	TF binding region
SLC3A2	TF binding region
ENSG00000269463	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000162231	Chromatin interaction
ENSG00000155090	Chromatin interaction
ENSG00000162188	Chromatin interaction
ENSG00000254772	Chromatin interaction
ENSG00000168002	Chromatin interaction
ENSG00000089597	Chromatin interaction
ENSG00000168000	Chromatin interaction
ENSG00000184224	Chromatin interaction
ENSG00000204922	Chromatin interaction
ENSG00000214753	Chromatin interaction
ENSG00000167792	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000162191	Chromatin interaction
ENSG00000162222	Chromatin interaction
ENSG00000185670	Chromatin interaction
ENSG00000185475	Chromatin interaction
ENSG00000162227	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000234857	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000168569	Chromatin interaction
ENSG00000269176	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs2730030	1.00[AMR][1000 genomes]
rs2730033	1.00[AMR][1000 genomes]
rs2956139	1.00[AMR][1000 genomes]
rs481272	0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs482331	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs489275	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs507101	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs519473	0.84[YRI][hapmap];0.85[AFR][1000 genomes]
rs560603	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs561385	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs561520	1.00[AMR][1000 genomes]
rs56226867	1.00[AMR][1000 genomes]
rs564587	0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs572513	0.83[YRI][hapmap]
rs577071	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs595108	1.00[AMR][1000 genomes]
rs694678	1.00[AMR][1000 genomes]
rs73487819	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73487834	0.96[AFR][1000 genomes]
rs73487878	0.85[AFR][1000 genomes]
rs73487879	0.85[AFR][1000 genomes]
rs73487880	0.87[AFR][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	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
8	nsv983154	chr11:62621265-62625410	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	133 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62618600-62621600	Strong transcription	Fetal Muscle Trunk	muscle
2	chr11:62618600-62621600	Strong transcription	Lung	lung
3	chr11:62618600-62622000	Genic enhancers	Primary B cells from peripheral blood	blood
4	chr11:62618800-62621400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:62618800-62623000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr11:62619000-62621800	Strong transcription	Aorta	Aorta
7	chr11:62619000-62623000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
8	chr11:62619000-62623200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
9	chr11:62619000-62623200	Transcr. at gene 5' and 3'	K562	blood
10	chr11:62619200-62621800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:62619200-62622200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
12	chr11:62619200-62622400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
13	chr11:62619200-62623000	Transcr. at gene 5' and 3'	NHEK	skin
14	chr11:62619200-62623200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr11:62619200-62623200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
16	chr11:62619200-62623200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
17	chr11:62619400-62622400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr11:62619400-62623000	Transcr. at gene 5' and 3'	Hela-S3	cervix
19	chr11:62619600-62621400	Genic enhancers	Primary B cells from cord blood	blood
20	chr11:62619600-62622600	Transcr. at gene 5' and 3'	HUVEC	blood vessel
21	chr11:62619600-62622800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
22	chr11:62619600-62623000	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
23	chr11:62619600-62623000	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
24	chr11:62619600-62623000	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
25	chr11:62619600-62623000	Transcr. at gene 5' and 3'	HMEC	breast
26	chr11:62619600-62623200	Transcr. at gene 5' and 3'	A549	lung
27	chr11:62619800-62622800	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr11:62620000-62623000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
29	chr11:62620000-62623200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr11:62620200-62623000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr11:62620400-62621600	Genic enhancers	Adipose Nuclei	Adipose
32	chr11:62620400-62622000	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
33	chr11:62620400-62622000	Transcr. at gene 5' and 3'	HepG2	liver
34	chr11:62620400-62622400	Transcr. at gene 5' and 3'	Psoas Muscle	Psoas
35	chr11:62620400-62622600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr11:62620400-62622800	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
37	chr11:62620400-62622800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:62620400-62622800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr11:62620400-62622800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:62620400-62623000	Transcr. at gene 5' and 3'	ES-UCSF4 Cell Line	embryonic stem cell
41	chr11:62620400-62623000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
42	chr11:62620400-62623000	Transcr. at gene 5' and 3'	NH-A	brain
43	chr11:62620400-62623200	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
44	chr11:62620400-62624000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
45	chr11:62620600-62621400	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
46	chr11:62620600-62621600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr11:62620600-62621800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells	blood
48	chr11:62620600-62621800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr11:62620600-62622800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
50	chr11:62620600-62622800	Transcr. at gene 5' and 3'	Fetal Heart	heart

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