Variant report

Variant	rs710163
Chromosome Location	chr9:95059804-95059805
allele	A/G
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:7)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:95057188..95059914-chr9:95129364..95132359,2	K562	blood:
2	chr9:95058975..95061785-chr9:95061896..95063797,3	MCF-7	breast:
3	chr9:95058426..95060967-chr9:95080944..95083546,2	MCF-7	breast:
4	chr9:95051112..95065542-chr9:95079443..95091389,38	K562	blood:
5	chr9:95052930..95062724-chr9:95083607..95090664,16	MCF-7	breast:
6	chr9:95036194..95038601-chr9:95058993..95061948,2	MCF-7	breast:
7	chr9:95008547..95010215-chr9:95057171..95060144,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IARS-1	chr9:95059640-95060168	NR_046106
2	lnc-IARS-1	chr9:95059766-95060168	NONHSAT133187

No data

Variant related genes	Relation type
ENSG00000198000	Chromatin interaction
ENSG00000188312	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10761149	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs10761156	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs10820952	0.92[CEU][hapmap]
rs1152757	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs1152759	0.89[CEU][hapmap]
rs1175788	0.88[CEU][hapmap]
rs1760318	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs1923599	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2025389	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs2031262	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs2147060	1.00[ASW][hapmap];0.89[CEU][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3174352	0.89[CEU][hapmap];0.83[TSI][hapmap]
rs331377	0.89[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs331379	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs331380	0.89[CEU][hapmap];0.81[TSI][hapmap]
rs331381	0.89[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3736835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3780346	0.85[CEU][hapmap]
rs3996311	0.92[CEU][hapmap]
rs471478	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs4743869	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs4744122	0.89[TSI][hapmap]
rs544396	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6651532	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs7028854	0.88[MKK][hapmap];0.91[TSI][hapmap]
rs7040860	0.82[EUR][1000 genomes]
rs7048808	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7867300	1.00[ASW][hapmap];0.89[CEU][hapmap];0.83[CHD][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9299402	0.86[EUR][1000 genomes]
rs9409664	0.92[CEU][hapmap];0.85[TSI][hapmap]

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	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers 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	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1045165	chr9:95057462-95138564	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs710163	CENPP	cis	parietal	SCAN
rs710163	ZNF484	cis	parietal	SCAN
rs710163	SPTLC1	cis	parietal	SCAN
rs710163	CENPP	cis	cerebellum	SCAN
rs710163	FANCC	cis	cerebellum	SCAN
rs710163	ZNF484	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95056800-95060400	Weak transcription	Aorta	Aorta
2	chr9:95056800-95086800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:95057000-95060000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr9:95057000-95060200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr9:95057000-95060200	Weak transcription	Fetal Muscle Leg	muscle
6	chr9:95057000-95060400	Weak transcription	Esophagus	oesophagus
7	chr9:95057000-95060400	Weak transcription	Left Ventricle	heart
8	chr9:95057000-95060800	Weak transcription	Colonic Mucosa	Colon
9	chr9:95057000-95061000	Weak transcription	Thymus	Thymus
10	chr9:95057000-95061400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:95057000-95061400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:95057000-95061400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:95057000-95061400	Weak transcription	Lung	lung
14	chr9:95057000-95061400	Weak transcription	Spleen	Spleen
15	chr9:95057000-95064800	Weak transcription	Ovary	ovary
16	chr9:95057000-95065000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr9:95057000-95070400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:95057000-95072600	Weak transcription	Gastric	stomach
19	chr9:95057000-95087000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr9:95057200-95060200	Weak transcription	Brain Anterior Caudate	brain
21	chr9:95057200-95060200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr9:95057200-95060400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr9:95057200-95060400	Weak transcription	Fetal Kidney	kidney
24	chr9:95057200-95060400	Weak transcription	Fetal Stomach	stomach
25	chr9:95057200-95061000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr9:95057200-95061400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr9:95057200-95061400	Weak transcription	Brain Angular Gyrus	brain
28	chr9:95057200-95063400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr9:95057200-95069000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr9:95057400-95060000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr9:95057400-95060200	Weak transcription	HSMMtube	muscle
32	chr9:95057400-95060200	Weak transcription	NHLF	lung
33	chr9:95057400-95060400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr9:95057400-95060400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr9:95057400-95061000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr9:95057400-95063200	Weak transcription	Fetal Brain Male	brain
37	chr9:95057400-95064600	Weak transcription	Right Ventricle	heart
38	chr9:95057400-95071200	Weak transcription	Small Intestine	intestine
39	chr9:95057800-95061400	Weak transcription	Pancreas	Pancrea
40	chr9:95057800-95063200	Weak transcription	Psoas Muscle	Psoas
41	chr9:95058000-95086200	Weak transcription	Stomach Mucosa	stomach
42	chr9:95058200-95061400	Weak transcription	Fetal Intestine Small	intestine
43	chr9:95058200-95073600	Strong transcription	Stomach Smooth Muscle	stomach
44	chr9:95058200-95073600	Strong transcription	HUVEC	blood vessel
45	chr9:95058200-95074600	Strong transcription	Fetal Thymus	thymus
46	chr9:95058200-95074800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr9:95058200-95085800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr9:95058400-95073400	Strong transcription	Fetal Lung	lung
49	chr9:95058400-95073600	Strong transcription	HMEC	breast
50	chr9:95058400-95074200	Strong transcription	Rectal Mucosa Donor 29	rectum

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