Variant report

Variant	rs10948176
Chromosome Location	chr6:44833913-44833914
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10456120	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10484625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10484626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10484627	1.00[YRI][hapmap]
rs10948171	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10948172	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]
rs10948185	1.00[YRI][hapmap]
rs10948192	1.00[YRI][hapmap]
rs10948196	1.00[JPT][hapmap]
rs11961316	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12190313	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12191977	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12193264	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12194924	0.81[AMR][1000 genomes]
rs12196188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs12198016	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12198308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12200892	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12202609	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12202698	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12202704	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12208332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12208605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs12209944	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12210292	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs12211922	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12212190	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12214435	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12214794	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12215095	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12215263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215971	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12525009	1.00[YRI][hapmap]
rs1329709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs1329711	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs1329714	0.82[YRI][hapmap]
rs17423748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1971482	1.00[YRI][hapmap]
rs2396372	1.00[YRI][hapmap]
rs3799973	0.91[YRI][hapmap]
rs3799976	1.00[YRI][hapmap]
rs3799977	1.00[YRI][hapmap]
rs3799979	1.00[YRI][hapmap]
rs3997499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4644056	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4711807	1.00[YRI][hapmap]
rs4714828	1.00[YRI][hapmap]
rs529125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55864280	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62436368	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62436369	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62436374	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62436375	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62436376	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62436395	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62436396	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62436411	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62437973	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62438018	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6909047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6924185	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs72865924	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7349931	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs755	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7765371	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs857601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs860741	0.95[CEU][hapmap]
rs9367210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9463042	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9463043	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9472365	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9472367	0.82[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10948176	SUPT3H	cis	cerebellum	SCAN
rs10948176	SUPT3H	cis	brain	seeQTL
rs10948176	SUPT3H	cis	parietal	SCAN
rs10948176	LOC100132354	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44823800-44836600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:44828400-44837800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr6:44833000-44834000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
4	chr6:44833200-44834200	Weak transcription	Fetal Intestine Small	intestine
5	chr6:44833600-44834200	Enhancers	Fetal Intestine Large	intestine
6	chr6:44833600-44849400	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr6:44833800-44834200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:44833800-44836400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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