Variant report

Variant	rs4237268
Chromosome Location	chr9:71458176-71458177
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRKACG-3	chr9:71458083-71458191	ENSG00000236733.1

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10115536	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10117744	0.80[ASN][1000 genomes]
rs10117946	0.86[ASN][1000 genomes]
rs10746942	0.82[AMR][1000 genomes]
rs10781232	0.82[CHB][hapmap];0.99[ASN][1000 genomes]
rs10869404	0.99[ASN][1000 genomes]
rs11143801	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11143802	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12686613	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1412988	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1414946	0.91[ASN][1000 genomes]
rs1537887	0.91[ASN][1000 genomes]
rs1556751	0.84[CEU][hapmap];0.92[GIH][hapmap];0.93[MEX][hapmap];0.82[AMR][1000 genomes]
rs17057642	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17057918	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17081050	1.00[CHB][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs1889150	0.80[ASW][hapmap];0.92[CEU][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1889937	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2027024	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[ASN][1000 genomes]
rs2039424	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2039425	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2039625	0.85[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2151421	0.93[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2151422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3750377	0.84[ASN][1000 genomes]
rs4259475	1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.99[ASN][1000 genomes]
rs4744712	0.81[CEU][hapmap];0.80[AMR][1000 genomes]
rs4745321	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.92[JPT][hapmap];0.86[LWK][hapmap];0.95[YRI][hapmap];0.99[ASN][1000 genomes]
rs4745351	0.92[ASN][1000 genomes]
rs4745354	0.90[ASN][1000 genomes]
rs4745359	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs61196668	0.90[ASN][1000 genomes]
rs6560398	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs6560407	0.90[ASN][1000 genomes]
rs7019684	0.90[ASN][1000 genomes]
rs7032651	0.92[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs7035999	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7039817	0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7045163	0.90[ASN][1000 genomes]
rs7046065	0.90[ASN][1000 genomes]
rs7046284	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs72512921	0.85[ASN][1000 genomes]
rs7851399	0.97[ASN][1000 genomes]
rs7861710	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865412	0.92[ASN][1000 genomes]
rs7869452	0.92[ASN][1000 genomes]
rs975123	0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][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	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh 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 miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS 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	27 gene(s)	inside rSNPs	diseases
9	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats 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
11	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv6548	chr9:71429527-71470917	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv466393	chr9:71453443-71704827	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv614547	chr9:71453443-71704827	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4237268	FAM5C	trans	cerebellum	SCAN
rs4237268	KLF9	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71435800-71464800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:71438000-71491200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr9:71440600-71466600	Weak transcription	Gastric	stomach
4	chr9:71441000-71478600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr9:71441600-71459800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr9:71443600-71458600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr9:71443600-71459000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr9:71445600-71458600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr9:71448200-71485600	Weak transcription	Stomach Mucosa	stomach
10	chr9:71449200-71459200	Weak transcription	Primary B cells from cord blood	blood
11	chr9:71452000-71458400	Weak transcription	Spleen	Spleen
12	chr9:71453800-71458600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:71455800-71459400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr9:71456800-71460000	Strong transcription	Fetal Intestine Small	intestine
15	chr9:71456800-71460600	Enhancers	Left Ventricle	heart
16	chr9:71457200-71458400	Weak transcription	Right Ventricle	heart
17	chr9:71457200-71458600	Weak transcription	Brain Anterior Caudate	brain
18	chr9:71457200-71458800	Weak transcription	Right Atrium	heart
19	chr9:71457200-71458800	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr9:71457200-71459000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr9:71457200-71459400	Weak transcription	Brain Hippocampus Middle	brain
22	chr9:71457400-71459800	Weak transcription	Fetal Heart	heart
23	chr9:71457600-71458200	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr9:71457600-71459200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr9:71457800-71458200	Weak transcription	Brain Angular Gyrus	brain
26	chr9:71457800-71458800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:71457800-71458800	Strong transcription	Fetal Intestine Large	intestine
28	chr9:71458000-71458400	Weak transcription	GM12878-XiMat	blood
29	chr9:71458000-71458800	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr9:71458000-71459200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr9:71458000-71459600	Enhancers	Lung	lung
32	chr9:71458000-71459800	Weak transcription	Aorta	Aorta

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