Variant report

Variant	rs57959812
Chromosome Location	chr10:52230372-52230373
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr10:52230359-52231152	T-47D	breast:	n/a	chr10:52230937-52230947 chr10:52230566-52230580
2	SIN3AK20	chr10:52230362-52231214	MCF-7	breast:	n/a	n/a
3	MAX	chr10:52229221-52230416	NB4	blood:	n/a	n/a
4	SMC3	chr10:52230235-52230440	GM12878	blood:	n/a	n/a
5	ELF1	chr10:52230300-52230961	MCF-7	breast:	n/a	n/a
6	EBF1	chr10:52230288-52230385	GM12878	blood:	n/a	n/a
7	KAP1	chr10:52230285-52231521	HEK293	kidney:	n/a	n/a
8	SIN3AK20	chr10:52230312-52231810	MCF-7	breast:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52224639..52228507-chr10:52228713..52230692,5	MCF-7	breast:
2	chr10:52229968..52233210-chr10:52382214..52385931,3	MCF-7	breast:
3	chr10:52229715..52232627-chr10:52381775..52384727,3	MCF-7	breast:
4	chr10:52228792..52231696-chr10:52270677..52273544,2	MCF-7	breast:
5	chr10:52186220..52188065-chr10:52229199..52231914,2	MCF-7	breast:
6	chr10:52174561..52178391-chr10:52227208..52231708,4	MCF-7	breast:
7	chr10:52218961..52222149-chr10:52229280..52232143,4	MCF-7	breast:
8	chr10:52176233..52179172-chr10:52229395..52232901,6	MCF-7	breast:

No data

Variant related genes	Relation type
SGMS1	TF binding region
ENSG00000225303	TF binding region
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10443954	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10508926	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10825903	0.80[EUR][1000 genomes]
rs10826032	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826101	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005316	1.00[ASN][1000 genomes]
rs11005345	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005595	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005612	0.81[EUR][1000 genomes]
rs11005708	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005730	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11005872	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005877	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005882	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005952	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005956	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006012	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11516712	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11591645	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11595661	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11598794	1.00[ASN][1000 genomes]
rs12354779	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12355439	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12357733	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12358247	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12360058	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177372	1.00[ASN][1000 genomes]
rs3001855	1.00[ASN][1000 genomes]
rs3001884	1.00[ASN][1000 genomes]
rs56251625	1.00[ASN][1000 genomes]
rs58969905	1.00[ASN][1000 genomes]
rs61739586	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071001	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7078586	1.00[ASN][1000 genomes]
rs7078940	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082728	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7091881	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7096968	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099535	1.00[ASN][1000 genomes]
rs72787008	1.00[ASN][1000 genomes]
rs72803755	1.00[ASN][1000 genomes]
rs74131268	1.00[ASN][1000 genomes]
rs74131270	1.00[ASN][1000 genomes]
rs74131283	1.00[ASN][1000 genomes]
rs74131284	1.00[ASN][1000 genomes]
rs74132707	0.81[EUR][1000 genomes]
rs74132723	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7477280	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7908093	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52192400-52230400	Weak transcription	HSMM	muscle
2	chr10:52208000-52240200	Weak transcription	Esophagus	oesophagus
3	chr10:52208400-52230400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr10:52215000-52230400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr10:52218000-52240200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr10:52218200-52230800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr10:52220000-52243600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr10:52220200-52230400	Weak transcription	Hela-S3	cervix
9	chr10:52220400-52237800	Weak transcription	Ovary	ovary
10	chr10:52220600-52230400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr10:52226800-52231000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr10:52227200-52230600	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr10:52227200-52231400	Enhancers	Primary T cells from cord blood	blood
14	chr10:52227400-52231200	Enhancers	Brain Anterior Caudate	brain
15	chr10:52227400-52231200	Enhancers	Brain Substantia Nigra	brain
16	chr10:52227400-52231200	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr10:52227400-52231200	Enhancers	Small Intestine	intestine
18	chr10:52227400-52231400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr10:52227600-52231000	Enhancers	Brain Cingulate Gyrus	brain
20	chr10:52227800-52231200	Enhancers	Fetal Intestine Large	intestine
21	chr10:52228200-52231000	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr10:52228200-52231200	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr10:52228400-52230800	Enhancers	Fetal Kidney	kidney
24	chr10:52228400-52231200	Enhancers	Brain Hippocampus Middle	brain
25	chr10:52228600-52230400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr10:52228600-52231000	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr10:52228600-52231200	Enhancers	NHDF-Ad	bronchial
28	chr10:52228800-52230400	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr10:52228800-52230400	Enhancers	Primary B cells from cord blood	blood
30	chr10:52228800-52230600	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr10:52228800-52231000	Enhancers	Colon Smooth Muscle	Colon
32	chr10:52228800-52231200	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr10:52228800-52231200	Enhancers	Fetal Intestine Small	intestine
34	chr10:52228800-52231400	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr10:52229000-52230400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr10:52229000-52230400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr10:52229000-52230400	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr10:52229000-52230600	Enhancers	Spleen	Spleen
39	chr10:52229000-52231000	Enhancers	Psoas Muscle	Psoas
40	chr10:52229000-52231200	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr10:52229000-52231200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr10:52229000-52231600	Enhancers	H9 Cell Line	embryonic stem cell
43	chr10:52229000-52231600	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr10:52229000-52231600	Enhancers	Brain Angular Gyrus	brain
45	chr10:52229000-52232400	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr10:52229200-52230400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr10:52229200-52230600	Weak transcription	K562	blood
48	chr10:52229200-52230800	Enhancers	Fetal Heart	heart
49	chr10:52229200-52231200	Enhancers	H1 Cell Line	embryonic stem cell
50	chr10:52229200-52231200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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