Variant report

Variant	rs1986972
Chromosome Location	chr8:10268805-10268806
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRSS55-4	chr8:10268611-10269075	NONHSAT124981

Extended variants
information (count: 51 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11249992	0.84[CEU][hapmap];0.81[GIH][hapmap]
rs11249995	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs11249996	0.88[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11249999	0.88[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11250001	0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11250002	0.87[CEU][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11779205	0.92[CEU][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11785061	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11989640	0.88[CEU][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12156350	0.92[CEU][hapmap]
rs12541491	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12543645	0.92[CEU][hapmap];0.92[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12547997	0.84[GIH][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes]
rs12548025	0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12550717	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13254942	0.96[CEU][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13264580	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17151899	0.80[JPT][hapmap]
rs17151903	0.96[CHD][hapmap]
rs17767186	0.85[MEX][hapmap]
rs2001337	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2001338	0.88[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3088186	0.80[CEU][hapmap];0.84[GIH][hapmap];0.80[TSI][hapmap]
rs34155841	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34381075	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34487437	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35060302	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35406700	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35472251	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35840352	0.81[EUR][1000 genomes]
rs4240645	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4292737	0.81[AMR][1000 genomes]
rs4316191	0.81[AMR][1000 genomes]
rs4841329	0.83[CEU][hapmap]
rs6999466	0.88[CEU][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7460436	0.95[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9650650	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9657539	0.88[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030934	chr8:10065169-10561161	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv890347	chr8:10153082-10331636	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1022994	chr8:10190618-10660122	Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv539466	chr8:10190618-10660122	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv527326	chr8:10199548-10320019	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1025557	chr8:10216726-10555187	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv917085	chr8:10237508-10828204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv465460	chr8:10241411-10290566	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
9	nsv610265	chr8:10241411-10290566	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
10	nsv610266	chr8:10250758-10294330	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv1019701	chr8:10254709-10279269	Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv890348	chr8:10265712-10289663	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
13	nsv610267	chr8:10268736-10526742	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1986972	FLJ10661	cis	cerebellum	SCAN
rs1986972	MFHAS1	cis	cerebellum	SCAN
rs1986972	C8orf79	cis	parietal	SCAN
rs1986972	DEFB136	cis	parietal	SCAN
rs1986972	PPP1R3B	cis	cerebellum	SCAN
rs1986972	C8orf13	cis	multi-tissue	Pritchard
rs1986972	CLDN23	cis	multi-tissue	Pritchard
rs1986972	FLJ10661	cis	parietal	SCAN
rs1986972	BLK	Cis_chr	lymphoblastoid	RTeQTL
rs1986972	C8orf5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10192600-10282400	Weak transcription	Gastric	stomach
2	chr8:10249000-10275200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr8:10257000-10274400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr8:10258200-10274400	Weak transcription	Esophagus	oesophagus
5	chr8:10261200-10273000	Weak transcription	Primary B cells from cord blood	blood
6	chr8:10261800-10274400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr8:10262000-10275200	Weak transcription	Psoas Muscle	Psoas
8	chr8:10263200-10271800	Weak transcription	Brain Hippocampus Middle	brain
9	chr8:10263600-10275200	Weak transcription	Pancreas	Pancrea
10	chr8:10263600-10283400	Weak transcription	Fetal Intestine Small	intestine
11	chr8:10263800-10269800	Weak transcription	Spleen	Spleen
12	chr8:10265000-10270200	Weak transcription	Liver	Liver
13	chr8:10266800-10270200	Enhancers	Brain Germinal Matrix	brain
14	chr8:10267000-10269600	Enhancers	Left Ventricle	heart
15	chr8:10267200-10273200	Enhancers	Fetal Brain Male	brain
16	chr8:10267600-10269200	Enhancers	Fetal Thymus	thymus
17	chr8:10267800-10269200	Enhancers	Fetal Muscle Leg	muscle
18	chr8:10267800-10269600	Enhancers	Primary T cells from cord blood	blood
19	chr8:10267800-10270600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr8:10267800-10271000	Enhancers	H1 Cell Line	embryonic stem cell
21	chr8:10267800-10271200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr8:10267800-10275200	Weak transcription	Right Atrium	heart
23	chr8:10268000-10269600	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr8:10268200-10269000	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr8:10268200-10269400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr8:10268200-10269400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr8:10268200-10269600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr8:10268200-10270400	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr8:10268200-10272000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr8:10268200-10275200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr8:10268400-10269000	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr8:10268400-10269000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr8:10268400-10269000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr8:10268400-10269000	Enhancers	NHEK	skin
35	chr8:10268400-10269200	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr8:10268400-10269400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr8:10268400-10269400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr8:10268600-10269000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr8:10268600-10269000	Enhancers	H9 Cell Line	embryonic stem cell
40	chr8:10268600-10269000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr8:10268600-10269000	Flanking Active TSS	Fetal Brain Female	brain
42	chr8:10268600-10270000	Enhancers	Brain Anterior Caudate	brain
43	chr8:10268600-10274400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr8:10268800-10269000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr8:10268800-10269000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr8:10268800-10269000	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr8:10268800-10269400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr8:10268800-10269400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr8:10268800-10270200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr8:10268800-10271800	Weak transcription	Brain Angular Gyrus	brain

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