Variant report

Variant	rs3016293
Chromosome Location	chr11:57430466-57430467
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:136)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:136 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:57430460-57430610	BJ	skin:	n/a	n/a
2	RAD21	chr11:57430328-57430702	GM12878	blood:	n/a	n/a
3	CTCF	chr11:57430387-57430590	GM12878	blood:	n/a	n/a
4	BHLHE40	chr11:57430448-57430644	K562	blood:	n/a	n/a
5	PAX5	chr11:57430369-57430568	GM12878	blood:	n/a	n/a
6	CTCF	chr11:57430406-57430605	GM10266	blood:	n/a	n/a
7	CTCF	chr11:57430405-57430578	GM10248	blood:	n/a	n/a
8	CTCF	chr11:57430380-57430530	GM12874	blood:	n/a	n/a
9	CTCF	chr11:57430360-57430510	GM12864	blood:	n/a	n/a
10	CTCF	chr11:57430420-57430570	K562	blood:	n/a	n/a
11	CTCF	chr11:57430420-57430570	BJ	skin:	n/a	n/a
12	RAD21	chr11:57430347-57430696	MCF-7	breast:	n/a	n/a
13	RAD21	chr11:57430347-57430661	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr11:57430360-57430510	HVMF	connective:	n/a	n/a
15	CTCF	chr11:57430460-57430610	GM12864	blood:	n/a	n/a
16	BCLAF1	chr11:57430382-57430689	GM12878	blood:	n/a	n/a
17	MAFK	chr11:57430450-57430566	Hela-S3	cervix:	n/a	n/a
18	RAD21	chr11:57430358-57430686	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr11:57430437-57430524	GM20000	blood:	n/a	n/a
20	CTCF	chr11:57430440-57430590	HMEC	breast:	n/a	n/a
21	CTCF	chr11:57430460-57430610	HMEC	breast:	n/a	n/a
22	RUNX3	chr11:57430312-57430617	GM12878	blood:	n/a	n/a
23	CTCF	chr11:57430380-57430530	GM12872	blood:	n/a	n/a
24	CTCF	chr11:57430360-57430510	GM06990	blood:	n/a	n/a
25	ZNF143	chr11:57430336-57430595	GM12878	blood:	n/a	n/a
26	RAD21	chr11:57430319-57430695	Hela-S3	cervix:	n/a	n/a
27	RUNX3	chr11:57430264-57430591	GM12878	blood:	n/a	n/a
28	CTCF	chr11:57430404-57430590	Medullo	brain:	n/a	n/a
29	RAD21	chr11:57430392-57430558	K562	blood:	n/a	n/a
30	CTCF	chr11:57430420-57430570	GM12878	blood:	n/a	n/a
31	RAD21	chr11:57430383-57430608	K562	blood:	n/a	n/a
32	PAX5	chr11:57430306-57430607	GM12878	blood:	n/a	n/a
33	CTCF	chr11:57430340-57430490	HA-sp	spinal cord:	n/a	n/a
34	CTCF	chr11:57430414-57430552	HUVEC	blood vessel:	n/a	n/a
35	CTCF	chr11:57430430-57430560	GM13977	blood:	n/a	n/a
36	RAD21	chr11:57430266-57430770	A549	lung:	n/a	n/a
37	RAD21	chr11:57430432-57430656	A549	lung:	n/a	n/a
38	CTCF	chr11:57430380-57430530	GM12873	blood:	n/a	n/a
39	CTCF	chr11:57430297-57430682	K562	blood:	n/a	n/a
40	CTCF	chr11:57430420-57430570	GM12873	blood:	n/a	n/a
41	SMC3	chr11:57430356-57430617	K562	blood:	n/a	n/a
42	CTCF	chr11:57430387-57430606	K562	blood:	n/a	n/a
43	CTCF	chr11:57430440-57430590	RPTEC	kidney:	n/a	n/a
44	CTCF	chr11:57430420-57430570	GM12865	blood:	n/a	n/a
45	CTCF	chr11:57430439-57430568	NHEK	skin:	n/a	n/a
46	CTCF	chr11:57430380-57430530	GM12865	blood:	n/a	n/a
47	RAD21	chr11:57430382-57430572	GM12878	blood:	n/a	n/a
48	CTCF	chr11:57430420-57430570	GM12864	blood:	n/a	n/a
49	CTCF	chr11:57430387-57430597	HepG2	liver:	n/a	n/a
50	CTCF	chr11:57430360-57430510	MCF-7	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:57429911..57430515-chr11:57567834..57568398,2	MCF-7	breast:
2	chr11:57427400..57431333-chr11:57432768..57435307,4	MCF-7	breast:
3	chr11:57423642..57427041-chr11:57427345..57431533,5	K562	blood:
4	chr11:57430324..57432082-chr11:57433263..57435317,2	MCF-7	breast:
5	chr11:57427698..57431931-chr11:57435517..57438480,4	MCF-7	breast:
6	chr11:57430289..57430928-chr11:58281166..58281939,2	K562	blood:
7	chr11:57429293..57431231-chr11:57440462..57442351,2	K562	blood:

No data

Variant related genes	Relation type
ZDHHC5	TF binding region
ENSG00000156599	Chromatin interaction
ENSG00000172409	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10160797	1.00[AMR][1000 genomes]
rs12282980	1.00[AMR][1000 genomes]
rs1941721	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2911725	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2926660	0.89[AFR][1000 genomes]
rs2926663	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2956980	0.90[AFR][1000 genomes]
rs2956983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2956984	0.82[AFR][1000 genomes]
rs2969941	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2969942	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2969945	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs3016261	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3016262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3016263	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3016264	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs600251	0.89[AFR][1000 genomes]
rs603420	0.89[AFR][1000 genomes]
rs610801	0.89[AFR][1000 genomes]
rs621683	0.85[AFR][1000 genomes]
rs621731	0.85[AFR][1000 genomes]
rs635536	0.85[AFR][1000 genomes]
rs660400	0.89[AFR][1000 genomes]
rs682785	0.85[AFR][1000 genomes]
rs686303	0.84[AFR][1000 genomes]
rs7127878	1.00[AMR][1000 genomes]
rs7939745	1.00[AMR][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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 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	chr11:57426000-57434000	Weak transcription	Fetal Heart	heart
2	chr11:57426000-57434000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:57426000-57434200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:57426000-57434200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:57426400-57430600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr11:57426400-57431400	Strong transcription	Fetal Stomach	stomach
7	chr11:57426600-57430600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr11:57426600-57430600	Strong transcription	Fetal Muscle Trunk	muscle
9	chr11:57426800-57430600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:57426800-57430600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr11:57426800-57430600	Strong transcription	Adipose Nuclei	Adipose
12	chr11:57426800-57430600	Strong transcription	Fetal Intestine Large	intestine
13	chr11:57426800-57430600	Strong transcription	Placenta	Placenta
14	chr11:57426800-57430600	Strong transcription	HSMM	muscle
15	chr11:57426800-57430800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr11:57426800-57430800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr11:57426800-57430800	Strong transcription	Fetal Muscle Leg	muscle
18	chr11:57426800-57430800	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr11:57427000-57430600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr11:57427000-57430600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr11:57427000-57430600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:57427000-57430600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:57427000-57430600	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr11:57427000-57430600	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr11:57427000-57430600	Strong transcription	Liver	Liver
26	chr11:57427000-57430600	Strong transcription	Brain Anterior Caudate	brain
27	chr11:57427000-57430600	Strong transcription	Brain Cingulate Gyrus	brain
28	chr11:57427000-57430600	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr11:57427000-57430600	Strong transcription	Fetal Thymus	thymus
30	chr11:57427000-57430600	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr11:57427000-57430600	Strong transcription	Stomach Smooth Muscle	stomach
32	chr11:57427000-57430600	Strong transcription	Thymus	Thymus
33	chr11:57427000-57430600	Strong transcription	NHEK	skin
34	chr11:57427000-57430600	Strong transcription	NHLF	lung
35	chr11:57427000-57430600	Strong transcription	Osteobl	bone
36	chr11:57427000-57430800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr11:57427000-57430800	Strong transcription	Primary T cells from cord blood	blood
38	chr11:57427000-57430800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr11:57427000-57430800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr11:57427000-57430800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr11:57427000-57431200	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr11:57427000-57431200	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr11:57427000-57431800	Strong transcription	Fetal Brain Female	brain
44	chr11:57427200-57430600	Strong transcription	Spleen	Spleen
45	chr11:57427200-57431400	Strong transcription	Duodenum Mucosa	Duodenum
46	chr11:57427400-57430600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr11:57427400-57431400	Strong transcription	Lung	lung
48	chr11:57427400-57434000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr11:57427600-57430600	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr11:57427600-57434000	Weak transcription	NHDF-Ad	bronchial

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