Variant report

Variant	rs2031599
Chromosome Location	chr9:98065943-98065944
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98062229..98064595-chr9:98064596..98066110,2	MCF-7	breast:
2	chr9:98065148..98068101-chr9:98075705..98077262,2	K562	blood:
3	chr9:98064416..98067357-chr9:98070574..98072936,2	K562	blood:
4	chr9:98064416..98068474-chr9:98070574..98074570,5	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10115247	0.82[EUR][1000 genomes]
rs1027710	0.85[EUR][1000 genomes]
rs10739992	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10739993	0.81[EUR][1000 genomes]
rs10761377	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10761382	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs10821453	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10821454	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10821455	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[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10821458	0.85[EUR][1000 genomes]
rs10821459	0.85[EUR][1000 genomes]
rs10993490	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10993518	0.80[EUR][1000 genomes]
rs13295862	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17686583	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1979022	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2166402	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2282216	0.96[CEU][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs2297596	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2297597	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2404457	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3277	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34045846	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34532504	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35081772	0.82[EUR][1000 genomes]
rs3737142	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[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3780564	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3780567	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs3780568	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes]
rs3824486	0.88[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs3844341	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3852402	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4647382	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4647443	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4647459	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4647462	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[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4647475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4647528	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4647529	0.80[EUR][1000 genomes]
rs4647534	0.96[CEU][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs4743993	0.85[EUR][1000 genomes]
rs4744446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4744451	0.96[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4744454	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4744455	0.85[EUR][1000 genomes]
rs6479601	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7019043	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7023007	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7026047	0.85[EUR][1000 genomes]
rs7027204	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7034538	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7850958	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7854570	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs879492	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs881791	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs963774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2031599	PHF2	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98050200-98067400	Weak transcription	A549	lung
2	chr9:98055000-98068600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:98055400-98066000	Weak transcription	Fetal Muscle Leg	muscle
4	chr9:98059600-98067000	Weak transcription	GM12878-XiMat	blood
5	chr9:98059800-98068000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:98059800-98068600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:98060200-98067400	Weak transcription	HSMM	muscle
8	chr9:98060400-98075000	Weak transcription	NHEK	skin
9	chr9:98061000-98067200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr9:98061000-98068800	Weak transcription	Small Intestine	intestine
11	chr9:98061800-98067400	Weak transcription	Fetal Lung	lung
12	chr9:98063200-98068200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr9:98063400-98068200	Weak transcription	Osteobl	bone
14	chr9:98063400-98069800	Weak transcription	Fetal Kidney	kidney
15	chr9:98063600-98067800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr9:98063600-98068200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:98063800-98066600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr9:98063800-98066600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr9:98063800-98067400	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr9:98064000-98067400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:98064000-98068600	Weak transcription	Ovary	ovary
22	chr9:98064400-98066200	Enhancers	Fetal Thymus	thymus
23	chr9:98064400-98066400	Enhancers	Primary T cells from cord blood	blood
24	chr9:98064600-98066800	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr9:98064800-98068600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr9:98065000-98066000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr9:98065000-98066200	Weak transcription	Fetal Stomach	stomach
28	chr9:98065000-98066200	Enhancers	Spleen	Spleen
29	chr9:98065200-98066000	Weak transcription	HUVEC	blood vessel
30	chr9:98065200-98066400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:98065200-98067200	Weak transcription	NHLF	lung
32	chr9:98065400-98067400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr9:98065600-98066000	Enhancers	Psoas Muscle	Psoas
34	chr9:98065600-98066800	Enhancers	Thymus	Thymus
35	chr9:98065800-98066200	Enhancers	Left Ventricle	heart
36	chr9:98065800-98066400	Enhancers	Lung	lung
37	chr9:98065800-98066600	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr9:98065800-98067000	Enhancers	Primary T cells fromperipheralblood	blood

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