Variant report

Variant	rs1084385
Chromosome Location	chr6:71402220-71402221
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10447360	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1084382	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1084386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10945228	1.00[ASN][1000 genomes]
rs12196191	0.82[ASW][hapmap]
rs13207234	1.00[ASN][1000 genomes]
rs1413353	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17763641	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2347624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2460694	1.00[ASN][1000 genomes]
rs2504742	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2504746	1.00[ASN][1000 genomes]
rs4235862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6455376	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6455381	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740106	1.00[ASN][1000 genomes]
rs7750570	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9294880	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9346399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9446297	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997350	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv886147	chr6:71273253-71471863	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1084385	TNKS	trans	parietal	SCAN
rs1084385	RIMS1	cis	parietal	SCAN
rs1084385	COL19A1	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71383000-71410400	Weak transcription	Gastric	stomach
2	chr6:71384600-71408800	Weak transcription	Pancreas	Pancrea
3	chr6:71390400-71410000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:71395200-71403200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr6:71395800-71417400	Weak transcription	Small Intestine	intestine
6	chr6:71396200-71409000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:71396400-71408800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:71396400-71410600	Weak transcription	Fetal Heart	heart
9	chr6:71396600-71403400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr6:71396800-71403200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:71396800-71403200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr6:71396800-71403200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr6:71396800-71403200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:71396800-71410400	Weak transcription	Liver	Liver
15	chr6:71396800-71411000	Weak transcription	Adipose Nuclei	Adipose
16	chr6:71397400-71403200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:71398400-71414400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:71398800-71411000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:71399200-71403600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:71400800-71411000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr6:71401600-71403200	Weak transcription	Left Ventricle	heart
22	chr6:71401800-71403200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr6:71401800-71409200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:71402000-71403400	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr6:71402200-71402400	Enhancers	Primary T helper cells fromperipheralblood	blood

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