Variant report

Variant	rs4935165
Chromosome Location	chr10:52229422-52229423
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr10:52229001-52229551	SK-N-SH	brain:	n/a	chr10:52229274-52229283
2	SPI1	chr10:52229321-52229781	HL-60	blood:	n/a	chr10:52229708-52229715 chr10:52229705-52229718 chr10:52229707-52229716 chr10:52229531-52229538
3	MAX	chr10:52229221-52230416	NB4	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr10:52224639..52228507-chr10:52228713..52230692,5	MCF-7	breast:
2	chr10:52228792..52231696-chr10:52270677..52273544,2	MCF-7	breast:
3	chr10:52227475..52229594-chr10:52231830..52233869,2	K562	blood:
4	chr10:52186220..52188065-chr10:52229199..52231914,2	MCF-7	breast:
5	chr10:52174561..52178391-chr10:52227208..52231708,4	MCF-7	breast:
6	chr10:52218961..52222149-chr10:52229280..52232143,4	MCF-7	breast:
7	chr10:52179209..52181843-chr10:52226952..52229570,2	MCF-7	breast:
8	chr10:52176233..52179172-chr10:52229395..52232901,6	MCF-7	breast:
9	chr10:52226760..52229659-chr10:52383902..52385556,2	K562	blood:
10	chr10:52227177..52229638-chr10:52267267..52268794,2	K562	blood:
11	chr10:52227035..52229845-chr10:52267079..52268728,2	MCF-7	breast:
12	chr10:52227444..52229529-chr10:52230846..52232373,2	MCF-7	breast:

No data

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

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10458673	0.81[ASN][1000 genomes]
rs10508927	0.81[ASN][1000 genomes]
rs10508929	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10733968	0.81[EUR][1000 genomes]
rs10740684	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10763382	0.83[ASN][1000 genomes]
rs10763392	0.81[EUR][1000 genomes]
rs10763426	0.88[ASN][1000 genomes]
rs10763500	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10825859	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10825861	0.83[ASN][1000 genomes]
rs10825882	0.86[ASN][1000 genomes]
rs10825904	0.88[ASN][1000 genomes]
rs10825934	0.88[ASN][1000 genomes]
rs10825978	0.89[ASN][1000 genomes]
rs10825995	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10825996	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10826013	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10826033	0.98[ASN][1000 genomes]
rs10826036	0.99[ASN][1000 genomes]
rs11005356	0.81[ASN][1000 genomes]
rs11005418	0.81[ASN][1000 genomes]
rs11005579	0.87[ASN][1000 genomes]
rs11005614	0.88[ASN][1000 genomes]
rs11005621	0.89[ASN][1000 genomes]
rs11005761	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11005803	0.99[ASN][1000 genomes]
rs11005884	0.98[ASN][1000 genomes]
rs12217648	0.88[ASN][1000 genomes]
rs12219070	0.99[ASN][1000 genomes]
rs1884572	0.95[ASN][1000 genomes]
rs1916572	0.87[ASN][1000 genomes]
rs2144863	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273402	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2339400	0.81[EUR][1000 genomes]
rs2339401	0.81[EUR][1000 genomes]
rs2339503	0.97[ASN][1000 genomes]
rs2339507	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34122137	0.87[ASN][1000 genomes]
rs3739989	0.81[ASN][1000 genomes]
rs4935711	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4935728	0.92[ASN][1000 genomes]
rs7079881	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7086029	0.87[ASN][1000 genomes]
rs7090807	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7093878	0.80[EUR][1000 genomes]
rs7094029	0.80[EUR][1000 genomes]
rs7896315	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7920818	0.96[ASN][1000 genomes]
rs910817	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs927047	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs927048	0.95[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:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52192400-52230400	Weak transcription	HSMM	muscle
2	chr10:52197800-52229800	Weak transcription	Gastric	stomach
3	chr10:52208000-52240200	Weak transcription	Esophagus	oesophagus
4	chr10:52208200-52229600	Weak transcription	Right Ventricle	heart
5	chr10:52208400-52230400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr10:52212800-52229600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr10:52215000-52230400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr10:52217200-52229600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr10:52218000-52240200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr10:52218200-52230800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr10:52220000-52243600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr10:52220200-52230400	Weak transcription	Hela-S3	cervix
13	chr10:52220400-52229600	Weak transcription	Fetal Thymus	thymus
14	chr10:52220400-52229800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr10:52220400-52229800	Weak transcription	Lung	lung
16	chr10:52220400-52230200	Weak transcription	NHLF	lung
17	chr10:52220400-52237800	Weak transcription	Ovary	ovary
18	chr10:52220600-52229600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr10:52220600-52229600	Weak transcription	Left Ventricle	heart
20	chr10:52220600-52229800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr10:52220600-52230400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr10:52220800-52230000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr10:52221200-52229600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr10:52221600-52230000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr10:52224400-52229600	Weak transcription	Fetal Muscle Leg	muscle
26	chr10:52226800-52231000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr10:52227200-52230600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr10:52227200-52231400	Enhancers	Primary T cells from cord blood	blood
29	chr10:52227400-52231200	Enhancers	Brain Anterior Caudate	brain
30	chr10:52227400-52231200	Enhancers	Brain Substantia Nigra	brain
31	chr10:52227400-52231200	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr10:52227400-52231200	Enhancers	Small Intestine	intestine
33	chr10:52227400-52231400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr10:52227600-52231000	Enhancers	Brain Cingulate Gyrus	brain
35	chr10:52227800-52229600	Weak transcription	Pancreas	Pancrea
36	chr10:52227800-52229800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr10:52227800-52231200	Enhancers	Fetal Intestine Large	intestine
38	chr10:52228200-52229600	Enhancers	GM12878-XiMat	blood
39	chr10:52228200-52231000	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr10:52228200-52231200	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr10:52228400-52230200	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr10:52228400-52230800	Enhancers	Fetal Kidney	kidney
43	chr10:52228400-52231200	Enhancers	Brain Hippocampus Middle	brain
44	chr10:52228600-52229600	Enhancers	HSMMtube	muscle
45	chr10:52228600-52230400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr10:52228600-52231000	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr10:52228600-52231200	Enhancers	NHDF-Ad	bronchial
48	chr10:52228800-52229600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr10:52228800-52229800	Enhancers	NH-A	brain
50	chr10:52228800-52230000	Enhancers	HepG2	liver

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