Variant report

Variant	rs17496500
Chromosome Location	chr10:52353375-52353376
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	CBX3	chr10:52352607-52353614	K562	blood:	n/a	n/a
2	MYC	chr10:52352406-52353405	K562	blood:	n/a	n/a
3	CUX1	chr10:52352771-52353502	K562	blood:	n/a	n/a
4	MYC	chr10:52352415-52353632	K562	blood:	n/a	n/a
5	CTCF	chr10:52353300-52353450	HMF	breast:	n/a	n/a
6	JUND	chr10:52353369-52354174	K562	blood:	n/a	n/a
7	CEBPB	chr10:52353281-52354178	K562	blood:	n/a	n/a
8	ZNF384	chr10:52352707-52353450	K562	blood:	n/a	n/a
9	E2F6	chr10:52352250-52353454	K562	blood:	n/a	chr10:52352411-52352423 chr10:52352412-52352419 chr10:52352888-52352899 chr10:52352412-52352419 chr10:52352412-52352419
10	RCOR1	chr10:52352593-52353727	K562	blood:	n/a	n/a
11	CTCF	chr10:52353240-52353390	AG10803	skin:	n/a	n/a
12	JUN	chr10:52352465-52354346	K562	blood:	n/a	n/a
13	EP300	chr10:52353054-52354272	SK-N-SH	brain:	n/a	n/a
14	CEBPB	chr10:52353343-52354205	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:52342133..52345402-chr10:52352257..52355042,3	MCF-7	breast:
2	chr10:52351092..52355625-chr10:52355822..52361152,8	K562	blood:
3	chr10:52352956..52355914-chr10:52362254..52364953,3	K562	blood:
4	chr10:52352876..52355415-chr10:52360770..52364645,3	K562	blood:

Variant related genes	Relation type
RNU7-107P	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10508931	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826273	0.90[MEX][hapmap]
rs11006166	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11006179	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11006183	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11006185	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11006190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11006191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11006193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11006194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11006197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11006200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11006213	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];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11006219	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11006222	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006229	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.96[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]
rs11006233	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];0.96[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]
rs11006237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006358	0.90[MEX][hapmap]
rs11006433	0.90[MEX][hapmap]
rs11006477	0.90[MEX][hapmap]
rs11816013	1.00[YRI][hapmap]
rs1203382	0.86[CHB][hapmap]
rs1203386	0.86[CHB][hapmap]
rs1203394	0.86[CHB][hapmap]
rs1203403	0.82[CHB][hapmap]
rs1203407	0.86[CHB][hapmap]
rs1203409	0.85[CHB][hapmap]
rs1203410	0.86[CHB][hapmap]
rs12358348	0.90[MEX][hapmap]
rs16937319	1.00[YRI][hapmap]
rs1740761	0.86[CHB][hapmap]
rs17496403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17581567	0.90[MEX][hapmap];0.82[TSI][hapmap]
rs17582633	0.90[MEX][hapmap]
rs2221	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2983350	0.86[CHB][hapmap]
rs2983354	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2983357	1.00[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap]
rs2983359	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2983361	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2983368	0.86[CHB][hapmap]
rs3011773	0.86[CHB][hapmap]
rs3011782	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs3011788	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs3011790	1.00[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap]
rs3011791	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs3011792	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs3011793	1.00[CHB][hapmap]
rs3011794	1.00[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap]
rs3011797	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs3011801	1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs55841709	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7072826	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];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7099133	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921226	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];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52336800-52363000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr10:52338000-52356400	Weak transcription	Fetal Brain Female	brain
3	chr10:52338000-52363800	Weak transcription	Fetal Kidney	kidney
4	chr10:52338000-52367000	Weak transcription	Aorta	Aorta
5	chr10:52338200-52353600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr10:52338200-52353800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr10:52338600-52353400	Weak transcription	Brain Germinal Matrix	brain
8	chr10:52338600-52353600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr10:52340400-52360200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr10:52341200-52373000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr10:52341400-52355400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr10:52341400-52360200	Weak transcription	GM12878-XiMat	blood
13	chr10:52341800-52355000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr10:52341800-52362000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr10:52342600-52356400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr10:52342800-52360200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr10:52343400-52360600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr10:52343600-52356200	Weak transcription	Stomach Mucosa	stomach
19	chr10:52343600-52362200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr10:52343800-52360000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr10:52346000-52355400	Weak transcription	Colon Smooth Muscle	Colon
22	chr10:52346400-52358600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr10:52346600-52355400	Weak transcription	Psoas Muscle	Psoas
24	chr10:52346600-52363400	Weak transcription	Adipose Nuclei	Adipose
25	chr10:52346600-52363800	Weak transcription	Spleen	Spleen
26	chr10:52346800-52360600	Weak transcription	HUVEC	blood vessel
27	chr10:52347000-52353600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr10:52347000-52359600	Weak transcription	A549	lung
29	chr10:52348000-52363400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr10:52348200-52358400	Weak transcription	HepG2	liver
31	chr10:52348200-52360000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr10:52348400-52363000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr10:52349000-52354000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr10:52349000-52363200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr10:52349200-52360400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr10:52349200-52363200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr10:52349400-52358600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr10:52349400-52363000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr10:52349400-52363000	Weak transcription	Lung	lung
40	chr10:52349600-52353400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr10:52349600-52353400	Weak transcription	Brain Substantia Nigra	brain
42	chr10:52349600-52353800	Weak transcription	Fetal Stomach	stomach
43	chr10:52349600-52355000	Weak transcription	Gastric	stomach
44	chr10:52349600-52355000	Weak transcription	Ovary	ovary
45	chr10:52349600-52358400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr10:52349600-52359200	Weak transcription	Placenta	Placenta
47	chr10:52349600-52360000	Weak transcription	Fetal Intestine Large	intestine
48	chr10:52349600-52360200	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr10:52349600-52360200	Weak transcription	Fetal Intestine Small	intestine
50	chr10:52349600-52360200	Weak transcription	Fetal Muscle Leg	muscle

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