Variant report

Variant	rs6990363
Chromosome Location	chr8:48101793-48101794
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-1134I14.8.1-1	chr8:48100930-48104439	NONHSAT126435

Extended variants
information (count: 67 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10088563	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10108778	0.82[EUR][1000 genomes]
rs10282752	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10441557	0.81[EUR][1000 genomes]
rs10481350	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11136099	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11776212	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11776864	0.81[EUR][1000 genomes]
rs11778776	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11784662	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11786883	0.84[EUR][1000 genomes]
rs13260244	0.83[ASN][1000 genomes]
rs1587401	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1846505	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1846508	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1909446	0.84[ASN][1000 genomes]
rs1909447	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2355358	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2362555	0.82[EUR][1000 genomes]
rs2431089	0.83[EUR][1000 genomes]
rs2454590	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2454605	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35332377	0.87[ASW][hapmap];0.91[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs35931929	0.84[EUR][1000 genomes]
rs405896	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4128701	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4242449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4392906	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs445724	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4513988	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4872733	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4873011	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4873024	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4873040	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4873043	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4873045	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4873269	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs62538786	0.83[ASN][1000 genomes]
rs6420176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6473996	0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.80[EUR][1000 genomes]
rs6558201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6558202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6558203	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6980904	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6981445	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6988360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6995008	0.85[EUR][1000 genomes]
rs7003488	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7815757	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7831310	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7840984	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs967625	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025638	chr8:47361534-48176434	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv530881	chr8:47456285-48129198	Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	nsv1020467	chr8:47456484-48174712	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv539589	chr8:47456484-48174712	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv1028036	chr8:47531749-48256108	Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv1019289	chr8:47536056-48251883	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv539591	chr8:47536056-48251883	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	nsv530882	chr8:47620846-48223868	ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	nsv1015347	chr8:47698082-48318579	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	nsv539593	chr8:47698082-48318579	Active TSS Flanking Active TSS Weak transcription Strong transcription 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	34 gene(s)	inside rSNPs	diseases
11	esv3693377	chr8:47824261-48582964	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
12	nsv890847	chr8:47937950-48124855	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv916549	chr8:47982642-48223882	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv1031982	chr8:47997015-48110595	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv491863	chr8:48053825-48586176	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6990363	MCM4	cis	lymphoblastoid	seeQTL
rs6990363	SNAI2	cis	cerebellum	SCAN
rs6990363	KIAA0146	cis	parietal	SCAN
rs6990363	MCM4	cis	cerebellum	SCAN
rs6990363	SCN1B	trans	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48099800-48101800	Active TSS	Brain Angular Gyrus	brain
2	chr8:48099800-48102000	Active TSS	Fetal Brain Female	brain
3	chr8:48101000-48101800	Flanking Active TSS	Brain Anterior Caudate	brain
4	chr8:48101000-48103200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr8:48101000-48105600	Weak transcription	Ovary	ovary
6	chr8:48101000-48116000	Weak transcription	Gastric	stomach
7	chr8:48101200-48101800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr8:48101200-48101800	Enhancers	Brain Germinal Matrix	brain
9	chr8:48101200-48102400	Weak transcription	Brain Hippocampus Middle	brain
10	chr8:48101200-48103600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr8:48101200-48103600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr8:48101200-48103600	Weak transcription	Osteobl	bone
13	chr8:48101200-48103800	Weak transcription	NHDF-Ad	bronchial
14	chr8:48101200-48105600	Weak transcription	Spleen	Spleen
15	chr8:48101200-48109600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr8:48101200-48110800	Weak transcription	Aorta	Aorta
17	chr8:48101200-48111600	Weak transcription	Right Atrium	heart
18	chr8:48101200-48115000	Weak transcription	Pancreas	Pancrea
19	chr8:48101400-48101800	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr8:48101400-48102600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr8:48101400-48102600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr8:48101400-48102600	Weak transcription	Fetal Brain Male	brain
23	chr8:48101400-48105000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr8:48101600-48102400	Weak transcription	Brain Substantia Nigra	brain

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