Variant report

Variant	rs1417408
Chromosome Location	chr10:99298476-99298477
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:99260929..99263151-chr10:99296889..99298735,2	MCF-7	breast:
2	chr10:99297536..99299525-chr10:99302249..99303762,2	MCF-7	breast:
3	chr10:99293705..99296189-chr10:99297526..99301633,5	MCF-7	breast:
4	chr10:99296840..99298523-chr10:99309435..99312063,2	MCF-7	breast:
5	chr10:99258307..99260062-chr10:99297196..99299410,2	MCF-7	breast:
6	chr10:99297050..99299012-chr10:99300542..99302143,2	MCF-7	breast:
7	chr10:99298137..99300363-chr10:99331501..99333055,2	MCF-7	breast:
8	chr10:99296911..99299412-chr10:99301338..99303433,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000165887	Chromatin interaction
ENSG00000155229	Chromatin interaction
ENSG00000165886	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10748698	0.84[EUR][1000 genomes]
rs10748699	0.95[CEU][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs10748700	0.81[EUR][1000 genomes]
rs10882957	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882959	0.95[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs10882961	0.83[EUR][1000 genomes]
rs10882962	0.95[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs10882963	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10882965	0.82[EUR][1000 genomes]
rs10882967	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1107517	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1107518	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11189267	0.95[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs11189270	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11189274	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11189275	0.95[CEU][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs11189278	0.82[EUR][1000 genomes]
rs11189280	0.94[ASN][1000 genomes]
rs11189284	0.85[CEU][hapmap];0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs11511362	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11528108	0.81[EUR][1000 genomes]
rs11528109	0.81[EUR][1000 genomes]
rs11814566	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12219064	0.90[CEU][hapmap]
rs12221474	0.89[CEU][hapmap]
rs12243136	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12355384	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12357750	0.94[ASN][1000 genomes]
rs12415338	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12766074	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12767760	0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.98[ASN][1000 genomes]
rs12774288	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12775868	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12779451	0.83[ASN][1000 genomes]
rs12783481	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1572860	0.95[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs17108059	0.82[EUR][1000 genomes]
rs2282372	0.82[CHB][hapmap]
rs3814554	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3818910	0.85[CEU][hapmap]
rs4244325	0.85[ASN][1000 genomes]
rs4244326	0.83[ASN][1000 genomes]
rs4635019	0.82[EUR][1000 genomes]
rs4917774	0.91[CHB][hapmap]
rs4919105	0.86[CHB][hapmap]
rs4919108	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4919109	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68084394	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7075656	0.85[CHB][hapmap]
rs7077976	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7094973	0.90[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.85[ASN][1000 genomes]
rs7342022	0.83[ASN][1000 genomes]
rs7475470	0.82[EUR][1000 genomes]
rs7475851	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7902642	0.95[CEU][hapmap];0.83[TSI][hapmap]
rs7911122	0.98[ASN][1000 genomes]
rs7923541	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1036494	chr10:99267639-99345207	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv7508	chr10:99285375-99330501	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1417408	RRP12	cis	parietal	SCAN
rs1417408	WNT8B	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99277800-99301800	Weak transcription	Gastric	stomach
2	chr10:99278000-99302600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr10:99278200-99298800	Weak transcription	Aorta	Aorta
4	chr10:99278400-99301800	Weak transcription	Spleen	Spleen
5	chr10:99278600-99300200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr10:99281400-99302200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr10:99282200-99301800	Weak transcription	Pancreas	Pancrea
8	chr10:99282800-99299400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr10:99285200-99298600	Weak transcription	Right Atrium	heart
10	chr10:99286200-99299200	Weak transcription	Ovary	ovary
11	chr10:99290000-99299400	Weak transcription	Right Ventricle	heart
12	chr10:99292000-99298600	Weak transcription	Lung	lung
13	chr10:99293200-99298600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr10:99293200-99301800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr10:99293400-99298600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr10:99293400-99298800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr10:99293400-99298800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr10:99293400-99299400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr10:99293400-99299600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr10:99293400-99300400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr10:99293600-99298600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr10:99294000-99298600	Weak transcription	Psoas Muscle	Psoas
23	chr10:99294200-99298600	Weak transcription	Fetal Muscle Leg	muscle
24	chr10:99294400-99301800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr10:99294600-99298800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr10:99294800-99299400	Weak transcription	Esophagus	oesophagus
27	chr10:99295000-99298600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr10:99295000-99298600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr10:99295000-99299400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr10:99295200-99299600	Weak transcription	K562	blood
31	chr10:99295400-99302400	Weak transcription	Fetal Intestine Small	intestine
32	chr10:99296400-99299600	Weak transcription	Fetal Stomach	stomach
33	chr10:99296800-99298600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr10:99297000-99300400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr10:99297200-99300000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr10:99297200-99303600	Enhancers	Placenta	Placenta
37	chr10:99297400-99299400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr10:99297400-99300800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr10:99297400-99302200	Enhancers	HSMMtube	muscle
40	chr10:99297800-99300000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr10:99297800-99300800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr10:99297800-99301600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr10:99297800-99301800	Enhancers	Muscle Satellite Cultured Cells	--
44	chr10:99297800-99301800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr10:99297800-99301800	Enhancers	Osteobl	bone
46	chr10:99297800-99302800	Enhancers	NH-A	brain
47	chr10:99298200-99298600	Enhancers	Brain Anterior Caudate	brain
48	chr10:99298200-99298800	Enhancers	Brain Substantia Nigra	brain
49	chr10:99298200-99299400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr10:99298200-99300000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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