Variant report

Variant	rs12571898
Chromosome Location	chr10:52385954-52385955
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:52383376-52385992	U87	brain:	n/a	n/a
2	POLR2A	chr10:52381694-52385975	Hela-S3	cervix:	n/a	n/a
3	MXI1	chr10:52381308-52386209	SK-N-SH	brain:	n/a	chr10:52384448-52384457 chr10:52384446-52384455
4	POLR2A	chr10:52383370-52385992	U87	brain:	n/a	n/a
5	POLR2A	chr10:52383384-52385973	PANC-1	pancreas:	n/a	n/a
6	PML	chr10:52383431-52385981	K562	blood:	n/a	chr10:52385807-52385815 chr10:52385790-52385798
7	ZMIZ1	chr10:52383597-52385964	K562	blood:	n/a	n/a
8	ESRRA	chr10:52381544-52386146	GM12878	blood:	n/a	chr10:52383842-52383855
9	POLR2A	chr10:52381639-52385981	K562	blood:	n/a	n/a
10	POLR2A	chr10:52385731-52385970	SK-N-SH	brain:	n/a	n/a
11	RFX5	chr10:52383546-52385978	Hela-S3	cervix:	n/a	n/a
12	TBP	chr10:52383867-52385976	Hela-S3	cervix:	n/a	n/a
13	HEY1	chr10:52383344-52385968	HepG2	liver:	n/a	chr10:52384345-52384360 chr10:52385015-52385030 chr10:52383658-52383673 chr10:52383361-52383376
14	POLR2A	chr10:52383186-52386125	H1-hESC	embryonic stem cell:	n/a	n/a
15	ELF1	chr10:52385683-52385977	HepG2	liver:	n/a	n/a
16	HCFC1	chr10:52383148-52386037	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr10:52383429-52385994	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr10:52372893..52376676-chr10:52385065..52387133,3	K562	blood:
2	chr10:52342227..52348125-chr10:52381237..52386507,8	K562	blood:
3	chr10:52385766..52387938-chr10:52404777..52406730,2	K562	blood:
4	chr10:52381243..52386496-chr10:52418227..52421959,6	MCF-7	breast:
5	chr10:52382538..52386733-chr10:52497918..52501112,4	MCF-7	breast:
6	chr10:52358660..52367648-chr10:52378481..52386533,25	MCF-7	breast:
7	chr10:52103151..52105270-chr10:52383748..52386662,2	K562	blood:
8	chr10:52173619..52179913-chr10:52381938..52386991,6	K562	blood:
9	chr10:52385910..52390098-chr10:52396807..52399699,3	MCF-7	breast:
10	chr10:52343887..52348125-chr10:52383719..52386062,5	K562	blood:
11	chr10:52356810..52366659-chr10:52378806..52385975,25	MCF-7	breast:
12	chr10:52385385..52386943-chr10:52417956..52419960,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ASAH2B-2	chr10:52383739-52386623	NONHSAT013388

No data

Variant related genes	Relation type
SGMS1	TF binding region
ENSG00000231345	Chromatin interaction
ENSG00000251950	Chromatin interaction
ENSG00000204147	Chromatin interaction
ENSG00000198964	Chromatin interaction
ENSG00000230036	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12241969	1.00[EUR][1000 genomes]
rs12267258	1.00[EUR][1000 genomes]
rs12572578	0.85[CHB][hapmap];1.00[EUR][1000 genomes]
rs16906575	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16907261	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4615973	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55703887	1.00[EUR][1000 genomes]
rs55928478	1.00[EUR][1000 genomes]
rs56039956	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57040666	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57073115	1.00[EUR][1000 genomes]
rs57238750	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57253864	1.00[EUR][1000 genomes]
rs57574235	1.00[EUR][1000 genomes]
rs57871603	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60613759	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60974974	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61027189	1.00[EUR][1000 genomes]
rs61518314	1.00[EUR][1000 genomes]
rs61615406	1.00[EUR][1000 genomes]
rs7080895	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7083978	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7093159	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73318780	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73320893	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73320899	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74131448	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7908759	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][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	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52381200-52386000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr10:52381400-52386000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr10:52381400-52386200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr10:52381800-52386000	Active TSS	Fetal Intestine Large	intestine
5	chr10:52382200-52386000	Active TSS	NHDF-Ad	bronchial
6	chr10:52382400-52386000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr10:52382400-52386000	Active TSS	NHLF	lung
8	chr10:52382600-52386000	Active TSS	H1 Cell Line	embryonic stem cell
9	chr10:52382600-52386000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:52382600-52386000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr10:52382600-52386000	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr10:52382800-52386000	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr10:52383200-52386000	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr10:52383200-52386000	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr10:52383400-52386000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr10:52383600-52386000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr10:52383600-52386000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr10:52383600-52386000	Active TSS	Brain Germinal Matrix	brain
19	chr10:52383800-52386000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr10:52384800-52386000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:52385000-52386000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr10:52385200-52386000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr10:52385200-52386000	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr10:52385200-52386000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr10:52385200-52386000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr10:52385200-52386000	Flanking Active TSS	Liver	Liver
27	chr10:52385200-52386000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
28	chr10:52385200-52386000	Flanking Active TSS	Osteobl	bone
29	chr10:52385400-52386000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr10:52385400-52386000	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr10:52385400-52386000	Flanking Active TSS	Fetal Brain Female	brain
32	chr10:52385400-52386000	Flanking Active TSS	Fetal Kidney	kidney
33	chr10:52385400-52386000	Flanking Active TSS	GM12878-XiMat	blood
34	chr10:52385400-52386000	Flanking Active TSS	Hela-S3	cervix
35	chr10:52385400-52386000	Flanking Active TSS	HMEC	breast
36	chr10:52385400-52386000	Flanking Active TSS	HSMM	muscle
37	chr10:52385400-52386000	Flanking Active TSS	K562	blood
38	chr10:52385400-52392400	Weak transcription	Lung	lung
39	chr10:52385600-52386000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr10:52385600-52386000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr10:52385600-52386000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr10:52385600-52386000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr10:52385600-52386000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr10:52385600-52386400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr10:52385600-52386400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr10:52385600-52389200	Weak transcription	Ovary	ovary
47	chr10:52385600-52392200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr10:52385600-52392200	Weak transcription	Left Ventricle	heart
49	chr10:52385600-52392400	Weak transcription	Gastric	stomach
50	chr10:52385600-52393000	Weak transcription	Pancreas	Pancrea

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