Variant report

Variant	rs12337959
Chromosome Location	chr9:98072029-98072030
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98070196..98076913-chr9:98077454..98080836,13	K562	blood:
2	chr9:98064416..98068474-chr9:98070574..98074570,5	K562	blood:
3	chr9:98070528..98077616-chr9:98077726..98081396,9	MCF-7	breast:
4	chr9:98069917..98072451-chr9:98074616..98076565,2	MCF-7	breast:
5	chr9:98070320..98072476-chr9:98077911..98080883,2	MCF-7	breast:
6	chr9:98064416..98067357-chr9:98070574..98072936,2	K562	blood:

Variant related genes	Relation type
ENSG00000158169	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10283758	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10993479	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10993483	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10993503	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10993520	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1105979	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12338907	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12339700	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12341302	0.88[EUR][1000 genomes]
rs12342782	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12350646	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12352586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12377946	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1886992	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28658564	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs356659	0.85[TSI][hapmap]
rs4237226	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4647372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4647373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4647401	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4647404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4647421	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4647432	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4647441	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4743990	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4744444	0.84[AMR][1000 genomes]
rs4744445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4744453	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744457	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4744458	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4744460	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs554879	0.88[TSI][hapmap]
rs56134407	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62560523	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7357617	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879559	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.80[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	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12337959	PHF2	cis	cerebellum	SCAN
rs12337959	CTSL2	cis	cerebellum	SCAN
rs12337959	LOC57653	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98060400-98075000	Weak transcription	NHEK	skin
2	chr9:98066200-98075200	Weak transcription	Left Ventricle	heart
3	chr9:98066800-98074800	Weak transcription	Thymus	Thymus
4	chr9:98067000-98075200	Weak transcription	Lung	lung
5	chr9:98067800-98074200	Weak transcription	GM12878-XiMat	blood
6	chr9:98068400-98075200	Weak transcription	HMEC	breast
7	chr9:98068800-98075200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:98068800-98075200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:98068800-98075200	Weak transcription	Brain Hippocampus Middle	brain
10	chr9:98068800-98075200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr9:98068800-98075400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:98069000-98075000	Weak transcription	Fetal Stomach	stomach
13	chr9:98069000-98075200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:98069000-98075200	Weak transcription	Fetal Lung	lung
15	chr9:98069000-98075200	Weak transcription	HUVEC	blood vessel
16	chr9:98069000-98075200	Weak transcription	NHLF	lung
17	chr9:98069000-98077200	Weak transcription	Hela-S3	cervix
18	chr9:98069000-98077400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:98069000-98077400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr9:98069400-98075200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:98069400-98075200	Weak transcription	Pancreas	Pancrea
22	chr9:98069400-98075200	Weak transcription	Psoas Muscle	Psoas
23	chr9:98069800-98075000	Weak transcription	Colonic Mucosa	Colon
24	chr9:98070000-98074400	Weak transcription	Fetal Heart	heart
25	chr9:98070200-98074200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:98070200-98074200	Weak transcription	A549	lung
27	chr9:98070200-98075200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:98070400-98073800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:98070400-98073800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr9:98070400-98074400	Weak transcription	K562	blood
31	chr9:98070400-98074800	Weak transcription	Liver	Liver
32	chr9:98070400-98075000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr9:98070400-98075000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr9:98070400-98075000	Weak transcription	Stomach Mucosa	stomach
35	chr9:98070400-98075000	Weak transcription	HepG2	liver
36	chr9:98070400-98075200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr9:98070800-98075200	Weak transcription	Fetal Intestine Small	intestine
38	chr9:98071000-98075000	Weak transcription	Fetal Intestine Large	intestine
39	chr9:98071000-98075200	Weak transcription	Small Intestine	intestine

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