Variant report

Variant	rs17111041
Chromosome Location	chr10:97378038-97378039
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr10:97377861-97378142	T-47D	breast:	n/a	n/a
2	POLR2A	chr10:97377969-97378040	HepG2	liver:	n/a	n/a
3	FOXA1	chr10:97377937-97378148	T-47D	breast:	n/a	n/a
4	GATA3	chr10:97377878-97378223	T-47D	breast:	n/a	n/a
5	GATA3	chr10:97377904-97378283	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:97375956..97378752-chr10:97415049..97416983,2	MCF-7	breast:

Variant related genes	Relation type
ALDH18A1	TF binding region
ENSG00000059573	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10159941	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs10509687	1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs10748634	0.92[CHB][hapmap]
rs10748635	0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs10748636	0.86[ASN][1000 genomes]
rs10748637	0.92[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs10786228	0.84[CHB][hapmap]
rs10786230	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs10786235	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs10882646	0.92[CHB][hapmap]
rs10882653	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs10882664	0.85[CHB][hapmap]
rs10882665	0.85[CHB][hapmap]
rs10882670	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs11188414	0.84[CHB][hapmap]
rs11188441	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11188459	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs11188485	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11188488	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11596004	0.82[CHB][hapmap]
rs12262943	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1340837	0.87[JPT][hapmap]
rs1890187	1.00[ASN][1000 genomes]
rs1933166	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs1933169	0.84[CHB][hapmap]
rs1953710	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs2211002	0.92[CHB][hapmap]
rs2225892	0.85[ASN][1000 genomes]
rs2225893	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs2275273	0.85[CHB][hapmap]
rs3750700	0.85[CHB][hapmap]
rs3750701	0.85[CHB][hapmap]
rs3763705	0.84[ASN][1000 genomes]
rs3763706	0.86[ASN][1000 genomes]
rs3793748	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs3949478	0.85[CHB][hapmap]
rs4075311	0.86[JPT][hapmap]
rs4290159	0.91[CHB][hapmap]
rs4457685	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs4501930	0.85[CHB][hapmap]
rs473251	0.86[ASN][1000 genomes]
rs476373	0.83[ASN][1000 genomes]
rs482811	0.82[ASN][1000 genomes]
rs4917698	0.86[ASN][1000 genomes]
rs4918950	0.92[CHB][hapmap]
rs4918956	0.86[ASN][1000 genomes]
rs4918964	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs496426	0.92[CHB][hapmap]
rs497331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs501603	1.00[JPT][hapmap]
rs524084	0.87[ASN][1000 genomes]
rs556869	0.85[ASN][1000 genomes]
rs571505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6584026	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs6584028	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs7069234	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs7073723	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs7073936	0.84[ASN][1000 genomes]
rs7081414	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs7084741	0.86[EUR][1000 genomes]
rs7085059	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7894052	0.86[ASN][1000 genomes]
rs7905653	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs7909569	0.92[CHB][hapmap]
rs7915345	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs7918235	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes]
rs7920850	0.92[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs945958	0.92[CHB][hapmap]
rs951418	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526180	chr10:97332195-97511037	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97364000-97382000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr10:97364000-97409200	Strong transcription	Primary T cells from cord blood	blood
3	chr10:97364000-97411000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr10:97364400-97378600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr10:97364400-97378600	Strong transcription	Fetal Brain Female	brain
6	chr10:97364400-97378600	Strong transcription	Spleen	Spleen
7	chr10:97364400-97379000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr10:97364400-97403200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr10:97364600-97378600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr10:97364600-97378600	Strong transcription	Pancreas	Pancrea
11	chr10:97364600-97378800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr10:97364600-97378800	Strong transcription	NH-A	brain
13	chr10:97364600-97379000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr10:97364600-97379000	Strong transcription	GM12878-XiMat	blood
15	chr10:97364600-97388400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr10:97364800-97378600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr10:97364800-97378600	Strong transcription	Gastric	stomach
18	chr10:97364800-97378800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr10:97364800-97378800	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr10:97364800-97378800	Strong transcription	Osteobl	bone
21	chr10:97364800-97379000	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr10:97364800-97403400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr10:97364800-97411000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr10:97365000-97378200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr10:97365000-97378400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr10:97365000-97378600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr10:97365000-97378600	Strong transcription	Brain Germinal Matrix	brain
28	chr10:97365000-97378800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr10:97365000-97378800	Strong transcription	Adipose Nuclei	Adipose
30	chr10:97365000-97379000	Strong transcription	Dnd41	blood
31	chr10:97365000-97403000	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr10:97365000-97403400	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr10:97365200-97378600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr10:97365200-97378800	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr10:97365200-97378800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr10:97365200-97379000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr10:97365200-97379200	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr10:97365200-97379200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr10:97365200-97379800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr10:97365200-97382200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr10:97365400-97378600	Strong transcription	Lung	lung
42	chr10:97365400-97378800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr10:97365400-97378800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr10:97365400-97378800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr10:97365400-97378800	Strong transcription	NHEK	skin
46	chr10:97365400-97379000	Strong transcription	Fetal Muscle Trunk	muscle
47	chr10:97365600-97378800	Strong transcription	Fetal Muscle Leg	muscle
48	chr10:97365600-97380800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr10:97365800-97378600	Strong transcription	Brain Anterior Caudate	brain
50	chr10:97365800-97378800	Strong transcription	H9 Cell Line	embryonic stem cell

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