Variant report

Variant	rs9348198
Chromosome Location	chr6:167271460-167271461
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12216339	0.90[CEU][hapmap]
rs1536641	0.90[CEU][hapmap]
rs1536645	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2149086	0.95[ASN][1000 genomes]
rs2149087	0.93[EUR][1000 genomes]
rs2881194	0.94[MKK][hapmap];1.00[YRI][hapmap]
rs4710121	1.00[CEU][hapmap];0.82[LWK][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.93[EUR][1000 genomes]
rs4710122	0.93[EUR][1000 genomes]
rs4710124	0.85[CHB][hapmap]
rs4710127	0.85[CHB][hapmap];0.82[MEX][hapmap]
rs7746934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7747434	0.84[MKK][hapmap]
rs7754775	0.96[EUR][1000 genomes]
rs7767948	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9347162	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9347163	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9348200	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9355601	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9356528	0.89[MKK][hapmap];1.00[YRI][hapmap]
rs9356529	0.95[CEU][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9356530	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9356531	0.90[CEU][hapmap];0.83[TSI][hapmap]
rs9366065	0.83[MKK][hapmap];1.00[YRI][hapmap]
rs9366066	0.90[CEU][hapmap];0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1019381	chr6:167090236-167558598	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv538541	chr6:167090236-167558598	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1022866	chr6:167108740-167345629	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv482525	chr6:167151805-167324406	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv605327	chr6:167185674-167360389	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1027314	chr6:167194653-167355961	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv538542	chr6:167194653-167355961	Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv605332	chr6:167198027-167353701	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv948634	chr6:167200671-167838993	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
13	nsv605333	chr6:167201033-167321693	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1016940	chr6:167222633-167289747	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv886942	chr6:167245665-167282950	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	esv2761039	chr6:167263541-167273178	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9348198	RPS6KA2	cis	multi-tissue	Pritchard

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167249000-167272200	Weak transcription	Fetal Stomach	stomach
2	chr6:167251800-167272800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:167260400-167274400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:167262000-167275000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:167264600-167274400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr6:167264600-167275000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:167265600-167272000	Weak transcription	Primary T cells from cord blood	blood
8	chr6:167266000-167272600	Weak transcription	Brain Hippocampus Middle	brain
9	chr6:167266200-167273200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr6:167266200-167274800	Weak transcription	Brain Substantia Nigra	brain
11	chr6:167266400-167275200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:167266600-167275000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:167266800-167273000	Weak transcription	Brain Angular Gyrus	brain
14	chr6:167267200-167275400	Weak transcription	Pancreas	Pancrea
15	chr6:167267400-167272000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:167267400-167272800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:167267400-167274400	Weak transcription	Brain Germinal Matrix	brain
18	chr6:167269600-167272000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:167270400-167272600	Weak transcription	Brain Anterior Caudate	brain
20	chr6:167270400-167275400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:167271400-167272200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:167271400-167273800	Weak transcription	Brain Inferior Temporal Lobe	brain

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