Variant report

Variant	rs9457237
Chromosome Location	chr6:167318304-167318305
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FGFR1OP-1	chr6:167317788-167318323	XLOC_005539
2	lnc-FGFR1OP-1	chr6:167317788-167318557	NR_046644

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10946197	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12203820	1.00[ASN][1000 genomes]
rs12205779	1.00[ASN][1000 genomes]
rs13213697	1.00[CHB][hapmap]
rs13220568	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs57919503	0.94[EUR][1000 genomes]
rs60192750	0.94[EUR][1000 genomes]
rs60913241	0.94[EUR][1000 genomes]
rs62436419	1.00[ASN][1000 genomes]
rs62436761	1.00[ASN][1000 genomes]
rs62438869	1.00[ASN][1000 genomes]
rs71571466	1.00[ASN][1000 genomes]
rs73254673	0.94[EUR][1000 genomes]
rs9457243	1.00[ASN][1000 genomes]
rs9459797	0.94[EUR][1000 genomes]
rs9459809	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv482507	chr6:167282376-167474915	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking 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	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9457237	RPS6KA2	cis	multi-tissue	Pritchard

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167297800-167320400	Weak transcription	Primary B cells from cord blood	blood
2	chr6:167298200-167320800	Weak transcription	Primary T cells from cord blood	blood
3	chr6:167315400-167320000	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr6:167315400-167321200	Weak transcription	Gastric	stomach
5	chr6:167315800-167320400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr6:167315800-167341600	Weak transcription	Pancreas	Pancrea
7	chr6:167316400-167320400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr6:167316600-167318800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:167316600-167318800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:167316800-167318600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr6:167316800-167318800	Enhancers	Fetal Brain Male	brain
12	chr6:167317200-167318600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:167317200-167318800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:167317200-167319400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr6:167317400-167318400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:167317400-167318400	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr6:167317400-167318800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:167317600-167318400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:167317600-167318600	Enhancers	H1 Cell Line	embryonic stem cell
20	chr6:167317800-167318400	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr6:167317800-167318400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:167317800-167318400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:167317800-167318400	Enhancers	Fetal Heart	heart
24	chr6:167317800-167318600	Active TSS	Brain Angular Gyrus	brain
25	chr6:167318000-167318400	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr6:167318000-167318400	Bivalent Enhancer	Brain Hippocampus Middle	brain
27	chr6:167318000-167318400	Enhancers	Fetal Brain Female	brain
28	chr6:167318000-167318800	Flanking Active TSS	Brain Anterior Caudate	brain
29	chr6:167318000-167318800	Bivalent Enhancer	Brain Substantia Nigra	brain
30	chr6:167318000-167320200	Weak transcription	GM12878-XiMat	blood
31	chr6:167318000-167321400	Weak transcription	Right Atrium	heart
32	chr6:167318200-167318400	Enhancers	Fetal Thymus	thymus
33	chr6:167318200-167318600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
34	chr6:167318200-167318600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
35	chr6:167318200-167318600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:167318200-167318600	Bivalent Enhancer	NH-A	brain
37	chr6:167318200-167319000	Enhancers	Brain Germinal Matrix	brain
38	chr6:167318200-167319800	Weak transcription	Spleen	Spleen
39	chr6:167318200-167320200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr6:167318200-167320400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:167318200-167320800	Enhancers	Brain Cingulate Gyrus	brain
42	chr6:167318200-167321000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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