Variant report

Variant	rs10948172
Chromosome Location	chr6:44777691-44777692
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10456120	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs10484625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10484626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs10807302	0.85[ASN][1000 genomes]
rs10948171	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12190313	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs12191977	0.81[EUR][1000 genomes]
rs12193264	0.80[EUR][1000 genomes]
rs12196188	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12197593	0.89[ASN][1000 genomes]
rs12198016	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs12200892	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12202609	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12202698	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202704	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12208332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs12208605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[TSI][hapmap]
rs12208621	0.92[ASN][1000 genomes]
rs12209944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210292	1.00[CHB][hapmap]
rs12211922	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12212190	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs12214435	0.85[EUR][1000 genomes]
rs12214794	0.81[EUR][1000 genomes]
rs12215095	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215181	0.85[ASN][1000 genomes]
rs12215263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12215971	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1329709	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1329711	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs17423748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs3997499	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs4644056	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55864280	0.81[EUR][1000 genomes]
rs59107271	0.92[ASN][1000 genomes]
rs62436022	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62436368	0.82[EUR][1000 genomes]
rs62436369	0.88[EUR][1000 genomes]
rs62436374	0.88[EUR][1000 genomes]
rs62436375	0.88[EUR][1000 genomes]
rs62436376	0.87[EUR][1000 genomes]
rs62437973	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62438018	0.88[EUR][1000 genomes]
rs7349931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7765371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs857601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs860741	0.95[CEU][hapmap];0.88[ASN][1000 genomes]
rs9367210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs9463042	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463043	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472365	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472367	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant related diseases (count:1)

Disease	PMID	Source
Osteoarthritis	22763110	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10948172	LOC100132354	cis	cerebellum	SCAN
rs10948172	SUPT3H	cis	parietal	SCAN
rs10948172	SUPT3H	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44776200-44777800	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr6:44776200-44779000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:44776400-44779200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:44776800-44778000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:44777000-44777800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:44777000-44777800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:44777000-44777800	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr6:44777000-44777800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:44777200-44779000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr6:44777200-44779200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr6:44777200-44779400	Weak transcription	Dnd41	blood
12	chr6:44777200-44783200	Weak transcription	Fetal Kidney	kidney
13	chr6:44777400-44778800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr6:44777400-44779000	Weak transcription	Primary T cells from cord blood	blood
15	chr6:44777400-44796600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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