Variant report

Variant	rs17298010
Chromosome Location	chr8:125506558-125506559
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:125505250..125507101-chr8:125521050..125523864,2	MCF-7	breast:
2	chr8:125505264..125507454-chr8:125529508..125531618,2	MCF-7	breast:
3	chr8:125504505..125508229-chr8:125551294..125554363,3	MCF-7	breast:
4	chr8:125504585..125506725-chr8:125538257..125539787,2	K562	blood:
5	chr8:125505181..125507555-chr8:125507868..125509849,2	K562	blood:
6	chr8:125503534..125506808-chr8:125536853..125540308,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147684	Chromatin interaction
ENSG00000147687	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1131024	1.00[ASW][hapmap];0.87[CEU][hapmap];0.92[GIH][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13250890	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13254054	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13263130	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13264071	1.00[CEU][hapmap];0.92[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13269215	1.00[ASW][hapmap];0.87[CEU][hapmap];0.92[GIH][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13276295	1.00[CEU][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34008273	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34115246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34681068	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34684627	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34714561	0.82[EUR][1000 genomes]
rs35005670	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35135081	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35309726	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35419095	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4358788	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4457314	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4535724	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4540394	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6470248	1.00[LWK][hapmap]
rs7010902	1.00[ASW][hapmap];0.87[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7813473	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531508	chr8:125390194-125587953	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers 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 miRNA target site	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17298010	ZHX2	cis	cerebellum	SCAN
rs17298010	TRMT12	cis	multi-tissue	Pritchard
rs17298010	ZNF572	cis	cerebellum	SCAN
rs17298010	NSMCE2	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125488200-125515800	Weak transcription	Lung	lung
2	chr8:125488200-125550400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:125489000-125519800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr8:125489000-125531200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr8:125489000-125541200	Weak transcription	Gastric	stomach
6	chr8:125489000-125543400	Weak transcription	Small Intestine	intestine
7	chr8:125493200-125539400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr8:125496000-125512600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr8:125496600-125549600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr8:125496800-125513200	Weak transcription	Brain Angular Gyrus	brain
11	chr8:125496800-125521200	Weak transcription	Fetal Heart	heart
12	chr8:125496800-125547400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr8:125498000-125506600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr8:125498000-125506800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr8:125498200-125507600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr8:125498200-125508000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr8:125499000-125513200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr8:125499000-125537200	Weak transcription	Esophagus	oesophagus
19	chr8:125499200-125515800	Weak transcription	Right Ventricle	heart
20	chr8:125499800-125512600	Weak transcription	Aorta	Aorta
21	chr8:125499800-125515800	Weak transcription	Colon Smooth Muscle	Colon
22	chr8:125500000-125512600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr8:125500000-125526200	Weak transcription	Colonic Mucosa	Colon
24	chr8:125500000-125538000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr8:125500000-125538400	Weak transcription	Psoas Muscle	Psoas
26	chr8:125500000-125549600	Weak transcription	Fetal Brain Male	brain
27	chr8:125500200-125512600	Weak transcription	NHDF-Ad	bronchial
28	chr8:125500200-125530800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr8:125500400-125512800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr8:125500400-125526400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr8:125500600-125513800	Weak transcription	Fetal Kidney	kidney
32	chr8:125501600-125514800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr8:125501600-125514800	Weak transcription	GM12878-XiMat	blood
34	chr8:125501600-125516000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr8:125501600-125524600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr8:125501600-125535000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr8:125501600-125550000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr8:125501800-125514800	Weak transcription	HUVEC	blood vessel
39	chr8:125502000-125513200	Weak transcription	Left Ventricle	heart
40	chr8:125502000-125515800	Weak transcription	HSMMtube	muscle
41	chr8:125502400-125512600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr8:125502400-125514800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr8:125502600-125514000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr8:125503800-125513200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr8:125503800-125513200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr8:125503800-125514800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr8:125503800-125514800	Weak transcription	Brain Anterior Caudate	brain
48	chr8:125503800-125515800	Weak transcription	Thymus	Thymus
49	chr8:125503800-125518800	Weak transcription	Brain Hippocampus Middle	brain
50	chr8:125504000-125508400	Weak transcription	HSMM	muscle

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