Variant report

Variant	rs1203380
Chromosome Location	chr10:52231729-52231730
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
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	GATA3	chr10:52231254-52231747	T-47D	breast:	n/a	n/a
2	ZNF217	chr10:52231455-52231751	MCF-7	breast:	n/a	n/a
3	GATA3	chr10:52231342-52231785	MCF-7	breast:	n/a	n/a
4	GATA3	chr10:52230414-52232119	MCF-7	breast:	n/a	chr10:52230645-52230655
5	GATA3	chr10:52231222-52231801	MCF-7	breast:	n/a	n/a
6	GATA3	chr10:52231342-52231758	T-47D	breast:	n/a	n/a
7	EP300	chr10:52231365-52231822	MCF-7	breast:	n/a	n/a
8	NR2F2	chr10:52231293-52231801	MCF-7	breast:	n/a	n/a
9	SIN3AK20	chr10:52230312-52231810	MCF-7	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52229968..52233210-chr10:52382214..52385931,3	MCF-7	breast:
2	chr10:52229715..52232627-chr10:52381775..52384727,3	MCF-7	breast:
3	chr10:52186220..52188065-chr10:52229199..52231914,2	MCF-7	breast:
4	chr10:52218961..52222149-chr10:52229280..52232143,4	MCF-7	breast:
5	chr10:52176233..52179172-chr10:52229395..52232901,6	MCF-7	breast:
6	chr10:52227444..52229529-chr10:52230846..52232373,2	MCF-7	breast:

No data

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

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10082515	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1011881	0.86[ASW][hapmap];0.82[LWK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs1028534	0.91[JPT][hapmap]
rs10826014	0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs11005720	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11005782	0.99[ASN][1000 genomes]
rs1203379	0.84[EUR][1000 genomes]
rs1203383	0.83[TSI][hapmap]
rs1203385	0.82[YRI][hapmap]
rs1203391	0.83[TSI][hapmap]
rs1203427	0.83[TSI][hapmap]
rs1212555	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12569801	0.91[JPT][hapmap]
rs12569909	0.91[JPT][hapmap]
rs12573520	0.91[JPT][hapmap]
rs16937491	0.91[JPT][hapmap]
rs16937722	0.88[JPT][hapmap]
rs16937771	0.91[JPT][hapmap]
rs16937775	0.91[JPT][hapmap]
rs16937786	0.91[JPT][hapmap]
rs17179881	0.85[JPT][hapmap]
rs2024871	0.84[EUR][1000 genomes]
rs2064760	0.85[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs2983346	0.85[EUR][1000 genomes]
rs2983348	0.83[TSI][hapmap]
rs2983349	0.85[EUR][1000 genomes]
rs3011712	0.84[EUR][1000 genomes]
rs3011715	0.83[EUR][1000 genomes]
rs3011795	0.84[EUR][1000 genomes]
rs3739990	0.91[JPT][hapmap]
rs41427847	0.91[JPT][hapmap]
rs73332935	0.94[ASN][1000 genomes]
rs910818	0.91[JPT][hapmap];0.85[EUR][1000 genomes]
rs910819	0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs9416590	0.84[EUR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1203380	CSTF2T	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52208000-52240200	Weak transcription	Esophagus	oesophagus
2	chr10:52218000-52240200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr10:52220000-52243600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr10:52220400-52237800	Weak transcription	Ovary	ovary
5	chr10:52229000-52232400	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr10:52229400-52231800	Enhancers	Stomach Mucosa	stomach
7	chr10:52229800-52242600	Weak transcription	Thymus	Thymus
8	chr10:52229800-52244000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr10:52229800-52252000	Weak transcription	Aorta	Aorta
10	chr10:52230000-52233600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr10:52230000-52237600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr10:52230000-52240000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr10:52230400-52231800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr10:52230400-52233400	Weak transcription	Left Ventricle	heart
15	chr10:52230400-52233600	Weak transcription	Gastric	stomach
16	chr10:52230400-52233600	Weak transcription	Pancreas	Pancrea
17	chr10:52230400-52233600	Weak transcription	Right Ventricle	heart
18	chr10:52230400-52236200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr10:52230400-52236400	Weak transcription	Primary B cells from cord blood	blood
20	chr10:52230400-52236400	Weak transcription	Lung	lung
21	chr10:52230400-52240000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr10:52230600-52232200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr10:52230600-52233600	Weak transcription	Right Atrium	heart
24	chr10:52230600-52233600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr10:52230600-52236000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr10:52230600-52236400	Weak transcription	Fetal Thymus	thymus
27	chr10:52230600-52256400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr10:52230800-52232400	Weak transcription	Fetal Heart	heart
29	chr10:52231000-52232200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr10:52231000-52232200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr10:52231000-52232600	Weak transcription	Psoas Muscle	Psoas
32	chr10:52231000-52233400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr10:52231000-52235400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr10:52231000-52235800	Weak transcription	HSMM	muscle
35	chr10:52231000-52236200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr10:52231000-52236200	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr10:52231000-52236400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr10:52231000-52237600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr10:52231000-52239400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr10:52231200-52231800	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr10:52231200-52232200	Weak transcription	K562	blood
42	chr10:52231200-52232600	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr10:52231200-52233400	Weak transcription	Small Intestine	intestine
44	chr10:52231200-52233600	Weak transcription	Brain Anterior Caudate	brain
45	chr10:52231200-52233600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr10:52231200-52233600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr10:52231200-52235000	Weak transcription	Brain Hippocampus Middle	brain
48	chr10:52231200-52236200	Weak transcription	Fetal Lung	lung
49	chr10:52231200-52236400	Weak transcription	Primary B cells from peripheral blood	blood
50	chr10:52231200-52236400	Weak transcription	Liver	Liver

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