Variant report

Variant	rs55979088
Chromosome Location	chr11:62410197-62410198
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:62410039-62410314	K562	blood:	n/a	n/a
2	POLR2A	chr11:62410137-62410236	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:62410051-62410330	HepG2	liver:	n/a	n/a
4	ESR1	chr11:62410034-62410277	ECC-1	luminal epithelium:	n/a	n/a
5	ESR1	chr11:62410044-62410358	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr11:62410014-62410570	PFSK-1	brain:	n/a	n/a
7	ESR1	chr11:62409994-62410377	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr11:62410086-62410797	HepG2	liver:	n/a	n/a
9	POLR2A	chr11:62409015-62410339	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:62410183-62410233	SK-N-SH_RA	brain:	n/a
2	chr11:62410183-62410233	Jurkat	blood:	n/a
3	chr11:62410183-62410233	A549	lung:	n/a
4	chr11:62410183-62410233	NHDF-neo	bronchial:	n/a
5	chr11:62410183-62410233	SK-N-MC	brain:	n/a
6	chr11:62410183-62410233	HEK293	kidney:	embryo
7	chr11:62410183-62410233	PANC-1	pancreas:	n/a
8	chr11:62410183-62410233	Hela-S3	cervix:	n/a
9	chr11:62410183-62410233	ECC-1	luminal epithelium:	n/a
10	chr11:62410183-62410233	AG09319	gingival:	n/a
11	chr11:62410183-62410233	ProgFib	skin:	n/a
12	chr11:62410183-62410233	IMR90	lung:	fetal
13	chr11:62410183-62410233	K562	blood:	n/a
14	chr11:62410183-62410233	T-47D	breast:	n/a
15	chr11:62410183-62410233	AG04449	skin:	fetal
16	chr11:62410183-62410233	HCF	heart:	n/a
17	chr11:62410183-62410233	HCT-116	colon:	n/a
18	chr11:62410183-62410233	PrEC	prostate:	n/a
19	chr11:62410183-62410233	SK-N-SH	brain:	n/a
20	chr11:62410183-62410233	LNCaP	prostate:	n/a
21	chr11:62410183-62410233	HepG2	liver:	n/a
22	chr11:62410183-62410233	SAEC	small airway:	n/a
23	chr11:62410183-62410233	GM12892	blood:	n/a
24	chr11:62410183-62410233	HRPEpiC	eye:	n/a
25	chr11:62410183-62410233	NB4	blood:	n/a
26	chr11:62410183-62410233	AG09309	skin:	n/a
27	chr11:62410183-62410233	BJ	skin:	n/a
28	chr11:62410183-62410233	NT2-D1	testis:	n/a
29	chr11:62410183-62410233	HMEC	breast:	n/a
30	chr11:62410183-62410233	ovcar-3	ovarian:	n/a
31	chr11:62410183-62410233	NH-A	brain:	n/a
32	chr11:62410183-62410233	AG10803	skin:	n/a
33	chr11:62410183-62410233	AG04450	lung:	fetal
34	chr11:62410183-62410233	HRE	kidney:	n/a
35	chr11:62410183-62410233	HIPEpiC	eye:	n/a
36	chr11:62410183-62410233	PFSK-1	brain:	n/a
37	chr11:62410183-62410233	HNPCEpiC	eye:	n/a
38	chr11:62410183-62410233	GM12878	blood:	n/a
39	chr11:62410183-62410233	HCM	heart:	n/a
40	chr11:62410183-62410233	Hepatocyte	liver:	n/a
41	chr11:62410183-62410233	H1-hESC	embryonic stem cell:	embryo
42	chr11:62410183-62410233	RPTEC	kidney:	n/a
43	chr11:62410183-62410233	HPAEpiC	pulmonary alveolar:	n/a
44	chr11:62410183-62410233	HL-60	blood:	n/a
45	chr11:62410183-62410233	AoSMC	blood vessel:	n/a
46	chr11:62410183-62410233	HCPEpiC	choroid plexus:	n/a
47	chr11:62410183-62410233	GM06990	blood:	n/a
48	chr11:62410183-62410233	U87	brain:	n/a
49	chr11:62410183-62410233	GM19239	blood:	n/a
50	chr11:62410183-62410233	MCF10A-Er-Src	breast:	n/a

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62408831..62411676-chr11:62419118..62421748,2	MCF-7	breast:
2	chr11:62407005..62417562-chr11:62426315..62441135,36	MCF-7	breast:
3	chr11:62394644..62397079-chr11:62409070..62411933,3	MCF-7	breast:
4	chr11:62399453..62402282-chr11:62406868..62410378,5	K562	blood:
5	chr11:62360489..62362247-chr11:62408764..62411725,2	MCF-7	breast:
6	chr11:62391785..62394595-chr11:62407451..62410585,3	MCF-7	breast:
7	chr11:62388412..62391284-chr11:62406977..62410339,6	K562	blood:
8	chr11:62408382..62410502-chr11:62493708..62497125,3	K562	blood:
9	chr11:62408398..62410453-chr11:62416921..62418570,2	MCF-7	breast:
10	chr11:62368912..62370477-chr11:62408882..62410508,2	MCF-7	breast:

No data

Variant related genes	Relation type
GANAB	TF binding region
GANAB	CpG island
ENSG00000089597	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000234857	Chromatin interaction
ENSG00000214753	Chromatin interaction
ENSG00000162222	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000149541	Chromatin interaction
ENSG00000149480	Chromatin interaction
ENSG00000204922	Chromatin interaction
ENSG00000255432	Chromatin interaction
ENSG00000185085	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12286444	0.90[AFR][1000 genomes]
rs12292661	1.00[EUR][1000 genomes]
rs1799959	1.00[EUR][1000 genomes]
rs2956992	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2957121	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4343028	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4387351	1.00[EUR][1000 genomes]
rs631714	0.86[AFR][1000 genomes]
rs73502110	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs948683	1.00[EUR][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	nsv832182	chr11:62295575-62462848	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
5	nsv825939	chr11:62326083-62410577	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
6	nsv497903	chr11:62330308-62608042	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	489 gene(s)	inside rSNPs	diseases
7	nsv555174	chr11:62334096-62496519	Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	243 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	chr11:62390000-62413200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:62390400-62411800	Strong transcription	Fetal Intestine Small	intestine
3	chr11:62390600-62412600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr11:62390800-62412400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:62390800-62412400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr11:62391000-62412000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr11:62391200-62412400	Strong transcription	Fetal Stomach	stomach
8	chr11:62392400-62411800	Strong transcription	Fetal Muscle Leg	muscle
9	chr11:62400400-62412400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:62400600-62412600	Weak transcription	Fetal Heart	heart
11	chr11:62401800-62410200	Weak transcription	Stomach Mucosa	stomach
12	chr11:62402200-62413000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr11:62402600-62412400	Weak transcription	Small Intestine	intestine
14	chr11:62402600-62412600	Weak transcription	Esophagus	oesophagus
15	chr11:62404400-62411400	Strong transcription	HSMM	muscle
16	chr11:62405400-62413000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr11:62406000-62413000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:62406800-62410200	Weak transcription	HUVEC	blood vessel
19	chr11:62406800-62412400	Weak transcription	Fetal Brain Male	brain
20	chr11:62406800-62413000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr11:62407000-62411800	Weak transcription	Colonic Mucosa	Colon
22	chr11:62407000-62412000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr11:62407000-62412000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr11:62407000-62412400	Weak transcription	Right Atrium	heart
25	chr11:62407000-62412600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr11:62407200-62410200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr11:62407200-62410200	Weak transcription	Liver	Liver
28	chr11:62407200-62410200	Weak transcription	Brain Angular Gyrus	brain
29	chr11:62407200-62410200	Weak transcription	Brain Anterior Caudate	brain
30	chr11:62407200-62410200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr11:62407200-62410200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr11:62407200-62410200	Weak transcription	Ovary	ovary
33	chr11:62407200-62410200	Weak transcription	NHLF	lung
34	chr11:62407200-62410400	Weak transcription	Lung	lung
35	chr11:62407200-62411600	Weak transcription	Left Ventricle	heart
36	chr11:62407200-62411800	Weak transcription	Brain Hippocampus Middle	brain
37	chr11:62407200-62411800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr11:62407200-62412000	Weak transcription	Right Ventricle	heart
39	chr11:62407200-62412200	Weak transcription	Primary B cells from cord blood	blood
40	chr11:62407200-62412400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr11:62407200-62412400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr11:62407200-62412400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr11:62407200-62412600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:62407200-62412600	Weak transcription	HSMMtube	muscle
45	chr11:62407200-62413000	Weak transcription	Psoas Muscle	Psoas
46	chr11:62407200-62413200	Weak transcription	Aorta	Aorta
47	chr11:62407200-62413200	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr11:62407400-62410200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr11:62407400-62410200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr11:62407400-62410200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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