Variant report

Variant	rs6738288
Chromosome Location	chr2:10585164-10585165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:10583356-10586233	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:10583084-10586162	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr2:10584307-10585680	IMR90	lung:	n/a	n/a
4	POLR2A	chr2:10583278-10585641	K562	blood:	n/a	n/a
5	POLR2A	chr2:10584086-10585181	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr2:10578415-10586213	GM12878	blood:	n/a	n/a
7	SPI1	chr2:10585091-10586217	GM12878	blood:	n/a	chr2:10585298-10585307 chr2:10585728-10585737

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:10583289..10586276-chr2:10586900..10589856,4	MCF-7	breast:
2	chr2:10259839..10264771-chr2:10582056..10590038,19	K562	blood:
3	chr2:10584788..10589777-chr2:10826863..10830293,6	K562	blood:
4	chr2:10583602..10586485-chr2:10613524..10616092,2	K562	blood:
5	chr2:10584220..10586892-chr2:10686951..10688711,2	K562	blood:
6	chr2:10266406..10268179-chr2:10582965..10585269,2	K562	blood:
7	chr2:10574850..10580139-chr2:10582463..10585343,4	MCF-7	breast:
8	chr2:10580034..10581693-chr2:10583711..10585512,2	MCF-7	breast:
9	chr2:10359472..10362167-chr2:10583974..10586621,2	K562	blood:
10	chr2:10441275..10444094-chr2:10585125..10586626,2	MCF-7	breast:
11	chr2:10257984..10265070-chr2:10582045..10589780,17	K562	blood:
12	chr2:10177980..10179820-chr2:10584164..10586131,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000257135	TF binding region
ENSG00000171848	Chromatin interaction
ENSG00000257135	Chromatin interaction
ENSG00000272524	Chromatin interaction
ENSG00000115756	Chromatin interaction
ENSG00000115761	Chromatin interaction
ENSG00000206633	Chromatin interaction
ENSG00000115758	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10170147	1.00[EUR][1000 genomes]
rs10189026	1.00[EUR][1000 genomes]
rs10203520	1.00[EUR][1000 genomes]
rs10203529	1.00[EUR][1000 genomes]
rs10490729	1.00[CHB][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11897672	1.00[EUR][1000 genomes]
rs11903106	1.00[EUR][1000 genomes]
rs11904157	1.00[EUR][1000 genomes]
rs11904263	1.00[EUR][1000 genomes]
rs13401475	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16856239	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16856397	1.00[EUR][1000 genomes]
rs1804032	1.00[ASN][1000 genomes]
rs28362383	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28362406	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28362407	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28362418	0.89[ASW][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55955247	1.00[ASN][1000 genomes]
rs58248202	1.00[EUR][1000 genomes]
rs59876692	1.00[EUR][1000 genomes]
rs61684351	1.00[EUR][1000 genomes]
rs73163017	1.00[EUR][1000 genomes]
rs73917006	1.00[EUR][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	nsv530829	chr2:10357105-10655131	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
2	nsv873645	chr2:10537347-10612091	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv1007185	chr2:10540386-10791743	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv873646	chr2:10550517-10612091	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	esv1840383	chr2:10569021-10588903	Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv873647	chr2:10576424-10597858	Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
7	nsv873648	chr2:10584639-10599493	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	esv1819730	chr2:10585164-10591407	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 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	chr2:10573000-10587400	Weak transcription	Right Atrium	heart
2	chr2:10573800-10586800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:10577200-10587800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:10578200-10585200	Strong transcription	Brain Germinal Matrix	brain
5	chr2:10578400-10585400	Strong transcription	Fetal Intestine Small	intestine
6	chr2:10578600-10585200	Strong transcription	HSMMtube	muscle
7	chr2:10578600-10585400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr2:10578600-10585600	Strong transcription	A549	lung
9	chr2:10578800-10585200	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr2:10578800-10585200	Strong transcription	Duodenum Mucosa	Duodenum
11	chr2:10578800-10585200	Strong transcription	Fetal Stomach	stomach
12	chr2:10578800-10585200	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr2:10578800-10585400	Strong transcription	Osteobl	bone
14	chr2:10578800-10585600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:10578800-10585600	Strong transcription	Primary T cells from cord blood	blood
16	chr2:10579000-10585200	Strong transcription	Brain Inferior Temporal Lobe	brain
17	chr2:10579000-10585200	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:10579000-10585200	Strong transcription	HepG2	liver
19	chr2:10579000-10585400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:10579000-10585400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:10579000-10585400	Strong transcription	Fetal Intestine Large	intestine
22	chr2:10579000-10585600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:10579000-10585600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr2:10579200-10585200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:10579200-10585200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:10579200-10585200	Strong transcription	NHDF-Ad	bronchial
27	chr2:10579200-10585400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:10579200-10585600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:10579200-10585600	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:10579400-10585200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:10579400-10585200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:10579400-10585200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:10579400-10585200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr2:10579400-10585200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:10579400-10585200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:10579400-10585200	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:10579400-10585600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr2:10579600-10585400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr2:10579600-10585600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:10579600-10585600	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr2:10579600-10585600	Strong transcription	Primary hematopoietic stem cells	blood
42	chr2:10579600-10585600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:10579600-10585600	Strong transcription	Fetal Thymus	thymus
44	chr2:10579800-10585200	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr2:10579800-10585200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:10579800-10585200	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:10579800-10585200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:10579800-10585200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr2:10579800-10585200	Strong transcription	Left Ventricle	heart
50	chr2:10579800-10585600	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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