Variant report

Variant	rs10948192
Chromosome Location	chr6:44947321-44947322
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 151 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs1023089	0.85[EUR][1000 genomes]
rs1023090	0.84[JPT][hapmap]
rs1041332	0.84[JPT][hapmap]
rs10456119	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10484627	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs10948176	1.00[YRI][hapmap]
rs10948183	0.84[JPT][hapmap]
rs10948185	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10948186	0.84[JPT][hapmap]
rs10948187	0.84[JPT][hapmap]
rs10948188	0.81[CEU][hapmap]
rs10948190	0.84[JPT][hapmap]
rs10948193	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10948194	0.89[JPT][hapmap]
rs10948197	1.00[CEU][hapmap];0.89[JPT][hapmap];0.96[EUR][1000 genomes]
rs10948198	0.85[CEU][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs10948201	0.83[YRI][hapmap]
rs11964325	0.80[CEU][hapmap];0.83[JPT][hapmap]
rs11966936	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs11967188	1.00[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11968042	0.81[EUR][1000 genomes]
rs12190261	0.84[EUR][1000 genomes]
rs12190513	0.84[JPT][hapmap]
rs12193812	0.91[YRI][hapmap]
rs12196818	0.92[CEU][hapmap];0.84[JPT][hapmap];0.90[EUR][1000 genomes]
rs12198904	0.90[EUR][1000 genomes]
rs12205071	0.84[CEU][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs12207620	0.89[EUR][1000 genomes]
rs12208023	0.84[CEU][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs12208339	0.88[EUR][1000 genomes]
rs12208483	0.81[EUR][1000 genomes]
rs12208605	0.83[YRI][hapmap]
rs12209076	0.86[EUR][1000 genomes]
rs12209161	0.83[YRI][hapmap]
rs12214778	0.92[CEU][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes]
rs12215263	0.91[YRI][hapmap]
rs12524069	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12525009	1.00[CEU][hapmap];0.84[JPT][hapmap];0.91[YRI][hapmap];0.92[EUR][1000 genomes]
rs12526711	0.92[EUR][1000 genomes]
rs12529490	0.84[CEU][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs1284972	0.88[CEU][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs1284973	0.82[EUR][1000 genomes]
rs1284975	0.82[EUR][1000 genomes]
rs1284982	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs1284983	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs1284987	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs1284988	0.85[CEU][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes]
rs1284992	0.84[CEU][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes]
rs1285004	0.84[JPT][hapmap]
rs1285026	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs13202529	0.86[EUR][1000 genomes]
rs13207575	0.84[EUR][1000 genomes]
rs13211229	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13213412	0.87[EUR][1000 genomes]
rs13215618	0.84[JPT][hapmap]
rs13216116	0.84[JPT][hapmap]
rs1324532	0.84[CEU][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes]
rs1329710	0.89[JPT][hapmap]
rs1329713	0.84[JPT][hapmap]
rs1329714	0.87[CEU][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs1329716	0.89[JPT][hapmap]
rs1360197	0.89[JPT][hapmap]
rs1411148	0.84[JPT][hapmap]
rs1521355	0.84[JPT][hapmap]
rs1590864	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17424547	1.00[CEU][hapmap];0.84[JPT][hapmap];0.95[EUR][1000 genomes]
rs1748231	0.84[JPT][hapmap]
rs1748234	0.84[JPT][hapmap]
rs1748235	0.84[JPT][hapmap]
rs1831310	0.95[EUR][1000 genomes]
rs1886345	0.83[JPT][hapmap]
rs1937046	0.84[CEU][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs1937047	0.81[EUR][1000 genomes]
rs1971482	1.00[CEU][hapmap];0.84[JPT][hapmap];0.92[YRI][hapmap];0.91[EUR][1000 genomes]
rs1980265	0.83[JPT][hapmap]
rs2038765	0.91[YRI][hapmap]
rs2186062	0.85[CEU][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs2396369	0.84[JPT][hapmap]
rs2396371	0.84[JPT][hapmap]
rs2396372	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.96[EUR][1000 genomes]
rs34808716	0.90[EUR][1000 genomes]
rs35357222	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35813980	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3778507	0.84[JPT][hapmap]
rs3799973	0.82[CEU][hapmap];0.83[YRI][hapmap]
rs3799976	1.00[CEU][hapmap];0.91[YRI][hapmap];0.86[EUR][1000 genomes]
rs3799977	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs3799979	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs3799981	0.84[JPT][hapmap]
rs3799986	0.84[JPT][hapmap]
rs4398713	0.84[JPT][hapmap]
rs4412189	0.85[CEU][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs4711805	0.89[EUR][1000 genomes]
rs4711807	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4714828	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs4714830	1.00[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4714832	0.95[EUR][1000 genomes]
rs4714836	0.84[CEU][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs494982	0.84[JPT][hapmap]
rs538801	0.84[JPT][hapmap]
rs55893720	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62438007	0.89[EUR][1000 genomes]
rs636845	0.84[JPT][hapmap]
rs6458414	0.80[EUR][1000 genomes]
rs6458415	0.84[JPT][hapmap]
rs6458418	0.85[EUR][1000 genomes]
rs6458419	0.84[JPT][hapmap]
rs6458423	0.84[JPT][hapmap]
rs6899378	0.84[JPT][hapmap]
rs6899845	0.84[JPT][hapmap]
rs6922660	0.84[JPT][hapmap]
rs6922772	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs6923436	0.81[EUR][1000 genomes]
rs6924185	0.83[YRI][hapmap]
rs6925017	0.89[JPT][hapmap]
rs6925467	0.88[CEU][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs7739928	0.83[JPT][hapmap]
rs7742360	0.84[JPT][hapmap]
rs7749865	1.00[CEU][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7758031	0.84[EUR][1000 genomes]
rs7763421	0.84[CEU][hapmap];0.89[JPT][hapmap]
rs7763450	0.85[CEU][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs7764102	0.82[EUR][1000 genomes]
rs7775717	0.90[JPT][hapmap]
rs9357464	0.90[JPT][hapmap]
rs9357469	0.84[JPT][hapmap]
rs9357470	0.84[JPT][hapmap]
rs9367210	0.91[YRI][hapmap]
rs9367214	0.84[JPT][hapmap]
rs9369529	0.85[CEU][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs9381365	0.84[JPT][hapmap]
rs9395065	0.88[CEU][hapmap];0.89[JPT][hapmap]
rs9472407	0.89[JPT][hapmap]
rs9472409	0.84[JPT][hapmap]
rs9472416	0.90[JPT][hapmap]
rs969211	0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs976699	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885861	chr6:44837356-45043618	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv1024370	chr6:44878053-45251451	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	esv2758051	chr6:44879791-45056758	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv2759423	chr6:44879791-45056758	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv885862	chr6:44890760-45083966	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv885863	chr6:44890760-45083966	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv885864	chr6:44890760-45198796	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
10	nsv462938	chr6:44909515-45008779	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv470817	chr6:44909515-45008779	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv603007	chr6:44909515-45008779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1023018	chr6:44925393-45152912	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv538212	chr6:44925393-45152912	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10948192	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL
rs10948192	SUPT3H	cis	multi-tissue	Pritchard

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44939800-44951200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:44940800-44957000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:44946600-44955000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:44946600-44955000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr6:44947000-44948400	Enhancers	Fetal Heart	heart
6	chr6:44947200-44947400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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