Variant report

Variant	rs9486306
Chromosome Location	chr6:106661530-106661531
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11152974	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3804334	0.80[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3862832	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59762106	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9320155	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9480652	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9486301	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486302	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486304	0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486305	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486308	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486311	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9486312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9486314	1.00[ASW][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];0.85[YRI][hapmap]
rs9486315	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9486319	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs9486320	0.85[EUR][1000 genomes]

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	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1025900	chr6:106529777-106898421	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1018270	chr6:106531658-106908606	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv538399	chr6:106531658-106908606	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1035110	chr6:106557281-106802212	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv538400	chr6:106557281-106802212	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv1022855	chr6:106570926-106802072	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv538401	chr6:106570926-106802072	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv1019265	chr6:106587627-106727591	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv538402	chr6:106587627-106727591	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	nsv1025963	chr6:106593639-106848778	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
13	nsv1020047	chr6:106597828-106912047	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
14	nsv970664	chr6:106635267-106887670	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9486306	SOBP	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106612400-106662000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:106626800-106674800	Weak transcription	K562	blood
3	chr6:106628400-106675200	Weak transcription	Stomach Mucosa	stomach
4	chr6:106628800-106671200	Weak transcription	Fetal Intestine Small	intestine
5	chr6:106632000-106664600	Weak transcription	Psoas Muscle	Psoas
6	chr6:106633400-106662000	Weak transcription	Fetal Lung	lung
7	chr6:106644600-106663000	Weak transcription	Left Ventricle	heart
8	chr6:106645800-106695400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr6:106647400-106695200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:106648600-106663000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:106648800-106661800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr6:106649000-106663000	Weak transcription	NHDF-Ad	bronchial
13	chr6:106649000-106663200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:106649200-106695200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:106649200-106695400	Weak transcription	HMEC	breast
16	chr6:106649400-106664200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:106649400-106682400	Weak transcription	Primary T cells from cord blood	blood
18	chr6:106649600-106663000	Weak transcription	NH-A	brain
19	chr6:106649600-106683000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr6:106650000-106663800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:106650000-106674200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:106650000-106674600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr6:106650000-106695200	Weak transcription	NHEK	skin
24	chr6:106650400-106674800	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr6:106650400-106682600	Weak transcription	Dnd41	blood
26	chr6:106650600-106671600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:106653200-106661600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:106653400-106662200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr6:106653400-106662200	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr6:106656200-106662400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:106657000-106661800	Weak transcription	Brain Hippocampus Middle	brain
32	chr6:106657200-106662200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr6:106657400-106673600	Weak transcription	HSMM	muscle
34	chr6:106657400-106674200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr6:106657400-106675000	Weak transcription	Primary B cells from cord blood	blood
36	chr6:106657800-106683200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:106658200-106661600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:106658200-106667800	Weak transcription	GM12878-XiMat	blood
39	chr6:106658200-106689000	Weak transcription	Primary B cells from peripheral blood	blood
40	chr6:106658600-106664600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:106661000-106662800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:106661400-106662200	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr6:106661400-106662800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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