Variant report

Variant	rs7904410
Chromosome Location	chr10:97724247-97724248
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10219061	0.94[EUR][1000 genomes]
rs10219085	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10509696	0.85[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs10736095	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10736096	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs10786240	0.82[CHB][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap]
rs10786241	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs10786242	0.82[CHB][hapmap]
rs10786245	0.81[ASN][1000 genomes]
rs10786249	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10786250	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10882686	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs10882690	0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10882693	0.83[YRI][hapmap]
rs10882694	0.80[AFR][1000 genomes]
rs11188526	0.96[ASN][1000 genomes]
rs1336457	0.93[ASW][hapmap];0.95[LWK][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes]
rs1336458	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1360955	0.92[CEU][hapmap];0.94[CHB][hapmap];0.83[YRI][hapmap];0.93[EUR][1000 genomes]
rs2027200	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs4254003	0.81[ASN][1000 genomes]
rs4303172	0.82[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.81[ASN][1000 genomes]
rs4415682	0.81[ASN][1000 genomes]
rs4917718	0.92[CEU][hapmap];0.94[CHB][hapmap];0.80[CHD][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.93[EUR][1000 genomes]
rs4918981	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4918982	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7893361	0.96[CEU][hapmap];0.83[YRI][hapmap]
rs7903617	0.92[CEU][hapmap];0.94[CHB][hapmap];0.81[YRI][hapmap];0.94[EUR][1000 genomes]
rs7907620	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7908420	0.85[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7908691	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs7913576	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7913608	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7921331	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7922217	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs9633701	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv895908	chr10:97544513-97724247	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv2761619	chr10:97719520-97746180	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7904410	TCTN3	cis	lymphoblastoid	seeQTL
rs7904410	ENTPD1	cis	multi-tissue	Pritchard
rs7904410	ENTPD1	Cis_1M	lymphoblastoid	RTeQTL
rs7904410	ENTPD1	cis	lymphoblastoid	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97720800-97731400	Weak transcription	Left Ventricle	heart
2	chr10:97722600-97725400	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr10:97722800-97724600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr10:97722800-97725000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr10:97722800-97725000	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr10:97722800-97729200	Weak transcription	Aorta	Aorta
7	chr10:97723000-97724800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr10:97723000-97725400	Enhancers	Primary B cells from peripheral blood	blood
9	chr10:97723200-97724800	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr10:97723600-97724400	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr10:97723800-97724800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr10:97723800-97724800	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr10:97724000-97724600	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr10:97724000-97724600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr10:97724000-97724800	Enhancers	Primary T cells from cord blood	blood
16	chr10:97724000-97724800	Enhancers	Primary hematopoietic stem cells	blood
17	chr10:97724000-97725400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr10:97724000-97725400	Enhancers	GM12878-XiMat	blood

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