Variant report

Variant	rs230222
Chromosome Location	chr9:95265558-95265559
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95261329..95263829-chr9:95264776..95266744,2	K562	blood:
2	chr9:95264347..95266316-chr9:95432237..95434126,2	K562	blood:

Variant related genes	Relation type
ENSG00000127080	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10283572	0.83[JPT][hapmap]
rs10453241	0.81[JPT][hapmap]
rs10491806	1.00[YRI][hapmap]
rs1053446	0.81[JPT][hapmap]
rs10761154	0.84[JPT][hapmap]
rs10761156	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10761158	0.81[JPT][hapmap]
rs10820969	0.81[JPT][hapmap]
rs10820971	0.81[JPT][hapmap]
rs10820998	1.00[YRI][hapmap]
rs10992322	0.81[JPT][hapmap]
rs10992347	0.81[JPT][hapmap]
rs10992367	1.00[YRI][hapmap]
rs10992380	1.00[YRI][hapmap]
rs10992407	1.00[YRI][hapmap]
rs1152757	0.80[EUR][1000 genomes]
rs1152759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1175788	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12552866	0.80[AMR][1000 genomes]
rs1323523	1.00[YRI][hapmap]
rs1535754	0.81[JPT][hapmap]
rs1853468	1.00[YRI][hapmap]
rs1923599	0.93[CEU][hapmap]
rs1924243	0.81[JPT][hapmap]
rs2025388	0.81[JPT][hapmap]
rs2025389	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2031262	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2131919	1.00[YRI][hapmap]
rs2147060	1.00[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs2181712	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2274966	0.81[JPT][hapmap]
rs2398751	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2516567	0.81[JPT][hapmap]
rs3174352	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs331377	0.93[CEU][hapmap];0.83[TSI][hapmap]
rs331379	0.93[CEU][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs331380	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs331381	0.93[CEU][hapmap];0.83[TSI][hapmap]
rs3996311	0.80[EUR][1000 genomes]
rs4743869	0.80[EUR][1000 genomes]
rs4744126	0.80[EUR][1000 genomes]
rs4744133	0.81[JPT][hapmap]
rs504708	0.80[EUR][1000 genomes]
rs6479419	0.81[JPT][hapmap]
rs7020874	0.81[JPT][hapmap]
rs7022562	0.81[JPT][hapmap]
rs7023004	0.81[JPT][hapmap]
rs7026361	0.81[JPT][hapmap]
rs7037075	0.81[JPT][hapmap]
rs7037194	0.81[JPT][hapmap]
rs7045409	0.81[JPT][hapmap]
rs7047089	0.81[JPT][hapmap]
rs7467899	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7847929	0.81[JPT][hapmap]
rs7850432	0.81[JPT][hapmap]
rs7853859	0.81[JPT][hapmap]
rs7856147	1.00[YRI][hapmap]
rs7857502	1.00[YRI][hapmap]
rs7867300	1.00[CEU][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs912264	1.00[YRI][hapmap]
rs9299404	0.81[JPT][hapmap]
rs9409664	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9409667	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs971984	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1047337	chr9:95105638-95347484	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1049599	chr9:95170139-95265558	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	esv1822933	chr9:95255176-95293308	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs230222	ECM2	cis	cerebellum	SCAN
rs230222	CENPP	cis	cerebellum	SCAN
rs230222	FBP1	cis	parietal	SCAN
rs230222	ZNF484	cis	parietal	SCAN
rs230222	CENPP	cis	parietal	SCAN
rs230222	ZNF484	cis	cerebellum	SCAN
rs230222	FANCC	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95231800-95268800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:95246400-95267000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:95252200-95266400	Weak transcription	NHLF	lung
4	chr9:95252400-95266200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:95252600-95269400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr9:95255000-95274600	Weak transcription	Liver	Liver
7	chr9:95255400-95266600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr9:95255400-95269400	Weak transcription	Right Ventricle	heart
9	chr9:95256600-95266000	Weak transcription	Fetal Lung	lung
10	chr9:95256800-95267000	Weak transcription	Fetal Stomach	stomach
11	chr9:95257600-95266800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:95258200-95268000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:95258600-95268200	Weak transcription	Fetal Heart	heart
14	chr9:95261400-95268200	Weak transcription	Brain Substantia Nigra	brain
15	chr9:95261600-95265600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr9:95261600-95266000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr9:95261600-95266200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:95261600-95266200	Weak transcription	Right Atrium	heart
19	chr9:95261800-95265800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr9:95262200-95269800	Weak transcription	Fetal Thymus	thymus
21	chr9:95262200-95270000	Weak transcription	Brain Anterior Caudate	brain
22	chr9:95262400-95268200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr9:95263400-95267400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:95264200-95268200	Weak transcription	Brain Hippocampus Middle	brain
25	chr9:95264400-95266200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:95264400-95268200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr9:95264600-95266200	Weak transcription	Esophagus	oesophagus
28	chr9:95264600-95266600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr9:95264600-95266600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr9:95264600-95266600	Weak transcription	Aorta	Aorta
31	chr9:95264600-95266600	Weak transcription	HMEC	breast
32	chr9:95264600-95266600	Weak transcription	K562	blood
33	chr9:95264600-95267800	Weak transcription	HSMMtube	muscle
34	chr9:95264600-95268200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr9:95264600-95269000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr9:95264600-95270000	Weak transcription	Lung	lung
37	chr9:95264800-95265600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:95264800-95265800	Weak transcription	Adipose Nuclei	Adipose
39	chr9:95264800-95266000	Weak transcription	Colon Smooth Muscle	Colon
40	chr9:95264800-95266000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr9:95264800-95266200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr9:95264800-95266200	Weak transcription	Ovary	ovary
43	chr9:95264800-95266200	Weak transcription	NHEK	skin
44	chr9:95264800-95266400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr9:95264800-95266400	Weak transcription	Osteobl	bone
46	chr9:95264800-95266600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr9:95264800-95266600	Weak transcription	Fetal Muscle Leg	muscle
48	chr9:95264800-95266600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr9:95264800-95266600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr9:95264800-95266600	Weak transcription	NHDF-Ad	bronchial

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