Variant report

Variant	rs17128130
Chromosome Location	chr10:112670141-112670142
allele	C/T
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	POLR2A	chr10:112670083-112670150	Gliobla	brain:	n/a	n/a
2	POLR2A	chr10:112669871-112670292	MCF-7	breast:	n/a	n/a
3	POLR2A	chr10:112669544-112670912	GM12878	blood:	n/a	n/a
4	POLR2A	chr10:112669924-112670802	GM12891	blood:	n/a	n/a
5	POLR2A	chr10:112669694-112671743	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:112664593..112668677-chr10:112669632..112672354,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270589	TF binding region
ENSG00000214413	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11195397	0.88[TSI][hapmap]
rs11195405	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11195417	0.91[ASW][hapmap];0.85[JPT][hapmap]
rs11195419	0.91[ASW][hapmap];0.85[JPT][hapmap]
rs11558147	0.90[ASN][1000 genomes]
rs11592715	0.81[ASN][1000 genomes]
rs11599619	0.83[ASN][1000 genomes]
rs12569835	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12571756	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12572049	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17128212	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17128356	0.91[ASW][hapmap];0.87[CEU][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs2295992	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3750625	0.85[JPT][hapmap]
rs4391757	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55794717	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56233990	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56784382	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56946887	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58164562	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7067787	0.89[GIH][hapmap];0.88[TSI][hapmap]
rs7072811	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7073594	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7073880	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73343848	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73343859	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73343879	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73345956	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74156313	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7902347	0.81[ASN][1000 genomes]
rs7919389	0.90[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045608	chr10:112524813-112677557	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1041758	chr10:112552897-112677557	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1051566	chr10:112580049-112730573	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1035602	chr10:112636053-112781413	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1051327	chr10:112650316-112772917	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv540774	chr10:112650316-112772917	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv831985	chr10:112652089-112803103	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1047865	chr10:112660427-112730573	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17128130	SHOC2	cis	lymphoblastoid	seeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112632800-112678000	Weak transcription	Lung	lung
2	chr10:112632800-112678200	Weak transcription	Spleen	Spleen
3	chr10:112634800-112677400	Weak transcription	HUVEC	blood vessel
4	chr10:112644200-112678000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr10:112644800-112675000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr10:112646400-112676400	Weak transcription	K562	blood
7	chr10:112647200-112677400	Weak transcription	Fetal Brain Male	brain
8	chr10:112656200-112672200	Weak transcription	Fetal Heart	heart
9	chr10:112656200-112677400	Weak transcription	Stomach Mucosa	stomach
10	chr10:112656400-112676400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr10:112656400-112677600	Weak transcription	Right Ventricle	heart
12	chr10:112657200-112672400	Weak transcription	Fetal Intestine Small	intestine
13	chr10:112657200-112675000	Weak transcription	Ovary	ovary
14	chr10:112657400-112672800	Weak transcription	HepG2	liver
15	chr10:112657400-112677600	Weak transcription	Psoas Muscle	Psoas
16	chr10:112657400-112677600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr10:112657400-112677800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr10:112657400-112677800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr10:112657400-112678000	Weak transcription	Gastric	stomach
20	chr10:112657600-112677600	Weak transcription	Fetal Brain Female	brain
21	chr10:112659200-112676400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr10:112659400-112677600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr10:112659600-112677600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr10:112659800-112675800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr10:112660200-112676000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr10:112660400-112670200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr10:112660400-112675800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr10:112660400-112676200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr10:112660400-112677000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr10:112660600-112677200	Weak transcription	Dnd41	blood
31	chr10:112661000-112677000	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr10:112661000-112677200	Weak transcription	Fetal Intestine Large	intestine
33	chr10:112661200-112676400	Weak transcription	Aorta	Aorta
34	chr10:112661400-112671000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr10:112661600-112677600	Weak transcription	Brain Germinal Matrix	brain
36	chr10:112661800-112675000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr10:112661800-112676000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr10:112662000-112676000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr10:112662200-112675600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr10:112662200-112676400	Weak transcription	Adipose Nuclei	Adipose
41	chr10:112662200-112677200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr10:112662400-112671800	Weak transcription	NH-A	brain
43	chr10:112662400-112676200	Weak transcription	Liver	Liver
44	chr10:112662400-112676400	Weak transcription	Fetal Kidney	kidney
45	chr10:112662400-112676600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr10:112662600-112671800	Weak transcription	HSMMtube	muscle
47	chr10:112662600-112671800	Weak transcription	NHDF-Ad	bronchial
48	chr10:112663000-112676000	Weak transcription	A549	lung
49	chr10:112663200-112671600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr10:112663200-112671800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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