Variant report

Variant	rs17128212
Chromosome Location	chr10:112726492-112726493
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:112725818..112728345-chr10:112732470..112734478,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11195397	0.88[TSI][hapmap]
rs11195405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11195417	1.00[ASW][hapmap];0.95[JPT][hapmap]
rs11195419	0.83[ASW][hapmap];0.95[JPT][hapmap]
rs11558147	0.81[ASN][1000 genomes]
rs11592715	0.90[ASN][1000 genomes]
rs11599619	0.90[ASN][1000 genomes]
rs12569835	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12571756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12572049	0.88[ASN][1000 genomes]
rs17128130	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17128356	0.83[ASW][hapmap];0.87[CEU][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2295992	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3750625	0.95[JPT][hapmap]
rs4391757	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55794717	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56233990	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56784382	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56946887	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58164562	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7067787	0.93[GIH][hapmap];0.88[TSI][hapmap]
rs7072811	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7073594	0.91[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7073880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73343848	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73343859	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73343879	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73345956	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74156313	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7902347	0.90[ASN][1000 genomes]
rs7919389	0.86[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv1048809	chr10:112683822-112781413	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv1042020	chr10:112686323-112795159	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv1035422	chr10:112724159-112764594	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1048444	chr10:112724159-112795159	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17128212	SHOC2	cis	multi-tissue	Pritchard
rs17128212	SHOC2	cis	lymphoblastoid	seeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112682000-112732400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr10:112692600-112732400	Weak transcription	Fetal Intestine Large	intestine
3	chr10:112697200-112740200	Weak transcription	Thymus	Thymus
4	chr10:112697200-112745400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr10:112700600-112764000	Weak transcription	Placenta	Placenta
6	chr10:112701200-112726800	Weak transcription	Dnd41	blood
7	chr10:112702400-112754800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr10:112703800-112729000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr10:112705200-112789800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr10:112707200-112732200	Weak transcription	Pancreas	Pancrea
11	chr10:112707200-112732200	Weak transcription	NHEK	skin
12	chr10:112707200-112732400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:112707200-112737600	Weak transcription	Psoas Muscle	Psoas
14	chr10:112707200-112738800	Weak transcription	NH-A	brain
15	chr10:112707200-112755000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr10:112707200-112784200	Weak transcription	Left Ventricle	heart
17	chr10:112709000-112760000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr10:112710000-112736400	Weak transcription	HSMM	muscle
19	chr10:112711800-112735600	Weak transcription	Fetal Intestine Small	intestine
20	chr10:112712200-112732400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr10:112712600-112732400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr10:112712600-112732400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr10:112712600-112732400	Weak transcription	Esophagus	oesophagus
24	chr10:112712600-112737200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr10:112712600-112737600	Weak transcription	HSMMtube	muscle
26	chr10:112712600-112737800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr10:112712600-112751200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr10:112712600-112755000	Weak transcription	Fetal Thymus	thymus
29	chr10:112712800-112736600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr10:112712800-112738000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr10:112712800-112751600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr10:112713200-112727200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr10:112719400-112760800	Weak transcription	Fetal Muscle Leg	muscle
34	chr10:112719600-112732000	Weak transcription	A549	lung
35	chr10:112719800-112735800	Weak transcription	Fetal Stomach	stomach
36	chr10:112719800-112737600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr10:112719800-112759200	Weak transcription	Fetal Lung	lung
38	chr10:112720800-112737600	Weak transcription	Ovary	ovary
39	chr10:112721600-112730000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr10:112721600-112737600	Weak transcription	Fetal Heart	heart
41	chr10:112722200-112726800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr10:112722600-112732400	Weak transcription	Brain Substantia Nigra	brain
43	chr10:112722800-112728400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr10:112722800-112730600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr10:112722800-112736600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr10:112723200-112730800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr10:112723200-112783000	Weak transcription	Small Intestine	intestine
48	chr10:112723400-112727400	Weak transcription	HepG2	liver
49	chr10:112723400-112727800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr10:112723400-112732400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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