Variant report

Variant	rs9299582
Chromosome Location	chr10:52304280-52304281
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52303296..52304994-chr10:52312451..52315128,2	MCF-7	breast:
2	chr10:52303071..52304706-chr10:52310411..52312427,2	K562	blood:
3	chr10:52304249..52305900-chr10:52382183..52384834,2	MCF-7	breast:
4	chr10:52291845..52294288-chr10:52302987..52304879,2	K562	blood:
5	chr10:52291845..52294615-chr10:52303379..52304888,2	K562	blood:

Variant related genes	Relation type
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1010930	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10763535	0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs10763550	0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs10763560	0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs10763566	0.91[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs10826149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10826155	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10826159	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10826160	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826161	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[ASN][1000 genomes]
rs10826163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826165	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826166	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10826167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826170	0.94[ASN][1000 genomes]
rs10826228	0.90[ASN][1000 genomes]
rs11006084	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.98[ASN][1000 genomes]
rs11006114	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[ASN][1000 genomes]
rs11006118	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11006141	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006160	0.92[ASN][1000 genomes]
rs11006201	0.87[ASN][1000 genomes]
rs11006217	0.86[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs12415817	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[ASN][1000 genomes]
rs12415836	1.00[ASN][1000 genomes]
rs12572387	0.91[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs1884570	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144861	0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.94[ASN][1000 genomes]
rs2224249	0.91[ASW][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2339507	0.81[TSI][hapmap]
rs3011777	0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs34659292	1.00[ASN][1000 genomes]
rs36122110	1.00[ASN][1000 genomes]
rs4935173	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4935174	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4935711	0.81[TSI][hapmap]
rs4935733	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7074764	0.91[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs7078284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7088141	0.91[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs7094143	1.00[ASN][1000 genomes]
rs7893884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7900424	0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7902354	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7907260	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7915606	0.95[CHB][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7916397	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910817	0.81[TSI][hapmap]
rs927047	0.81[TSI][hapmap]
rs9919413	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[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:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52280200-52328000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr10:52296800-52306000	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr10:52297000-52304400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr10:52297000-52304600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr10:52297400-52306000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr10:52299000-52304400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr10:52299000-52305400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr10:52299000-52305400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr10:52299000-52310200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr10:52299200-52304600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr10:52299200-52305800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr10:52299200-52310200	Weak transcription	Pancreas	Pancrea
13	chr10:52299600-52320600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:52300200-52305000	Weak transcription	HepG2	liver
15	chr10:52300600-52310200	Weak transcription	Placenta	Placenta
16	chr10:52300800-52304600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr10:52300800-52304800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr10:52300800-52310800	Weak transcription	Gastric	stomach
19	chr10:52300800-52322800	Weak transcription	Primary B cells from cord blood	blood
20	chr10:52301400-52304800	Weak transcription	Psoas Muscle	Psoas
21	chr10:52301400-52306000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr10:52301400-52308600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr10:52301600-52304400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr10:52301600-52306000	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr10:52301600-52309200	Weak transcription	Ovary	ovary
26	chr10:52301600-52310200	Weak transcription	Left Ventricle	heart
27	chr10:52301600-52327200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr10:52302400-52306000	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr10:52302600-52305000	Enhancers	Brain Substantia Nigra	brain
30	chr10:52302600-52305200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr10:52302600-52306000	Enhancers	Primary T cells from cord blood	blood
32	chr10:52302800-52304400	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr10:52302800-52304800	Enhancers	Small Intestine	intestine
34	chr10:52302800-52306000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr10:52303000-52304400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr10:52303000-52304400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr10:52303000-52304600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr10:52303000-52305000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr10:52303000-52305200	Enhancers	GM12878-XiMat	blood
40	chr10:52303200-52310200	Weak transcription	Fetal Lung	lung
41	chr10:52303200-52310200	Weak transcription	Stomach Mucosa	stomach
42	chr10:52303200-52312200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr10:52303400-52304400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr10:52303400-52304400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr10:52303400-52304400	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr10:52303400-52304600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr10:52303400-52304800	Weak transcription	Primary B cells from peripheral blood	blood
48	chr10:52303400-52304800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr10:52303400-52309400	Weak transcription	Liver	Liver
50	chr10:52303400-52310200	Weak transcription	Spleen	Spleen

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