Variant report

Variant	rs10908578
Chromosome Location	chr1:153954674-153954675
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10127484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs10908526	0.83[AMR][1000 genomes]
rs11264573	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes]
rs11264621	0.86[AMR][1000 genomes]
rs11264736	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12117078	1.00[JPT][hapmap]
rs12142733	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs1591902	1.00[CHB][hapmap]
rs17364880	1.00[JPT][hapmap]
rs2252508	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes]
rs2790686	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap]
rs2841108	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap]
rs3001365	1.00[CHB][hapmap]
rs4845360	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4845586	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6661009	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6671362	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7414227	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs7521047	0.81[MEX][hapmap]
rs7522030	0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap]
rs7537213	0.86[MEX][hapmap]
rs9427318	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10908578	PSMD4	cis	parietal	SCAN
rs10908578	SLC27A3	cis	cerebellum	SCAN
rs10908578	S100A8	cis	parietal	SCAN
rs10908578	GATAD2B	cis	cerebellum	SCAN
rs10908578	FLG	cis	parietal	SCAN
rs10908578	S100A13	cis	lymphoblastoid	seeQTL
rs10908578	HAX1	cis	cerebellum	SCAN
rs10908578	SLC25A44	cis	parietal	SCAN
rs10908578	GBA	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153950800-153957200	Weak transcription	HSMM	muscle
2	chr1:153950800-153957400	Weak transcription	Stomach Mucosa	stomach
3	chr1:153950800-153957600	Weak transcription	Ovary	ovary
4	chr1:153950800-153957800	Weak transcription	Esophagus	oesophagus
5	chr1:153950800-153958000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:153950800-153958000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:153951000-153956000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:153951000-153957000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:153951000-153957200	Weak transcription	Colonic Mucosa	Colon
10	chr1:153951000-153957200	Weak transcription	Pancreas	Pancrea
11	chr1:153951000-153957600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:153951000-153957800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:153951200-153956800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:153951200-153956800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:153951200-153956800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr1:153951200-153956800	Weak transcription	Brain Substantia Nigra	brain
17	chr1:153951200-153956800	Weak transcription	Fetal Kidney	kidney
18	chr1:153951200-153957000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:153951200-153957000	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:153951200-153957000	Weak transcription	HSMMtube	muscle
21	chr1:153951200-153957200	Weak transcription	Right Ventricle	heart
22	chr1:153951200-153957200	Weak transcription	HMEC	breast
23	chr1:153951200-153957400	Weak transcription	NHEK	skin
24	chr1:153951400-153956400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:153951400-153956400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:153951400-153956600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:153951400-153956800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:153951400-153956800	Weak transcription	Brain Anterior Caudate	brain
29	chr1:153951400-153956800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:153951400-153956800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:153951400-153956800	Weak transcription	Right Atrium	heart
32	chr1:153951400-153956800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:153951400-153957000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:153951400-153957200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:153951400-153957400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:153951400-153957800	Weak transcription	Fetal Thymus	thymus
37	chr1:153951600-153955800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:153951600-153956800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:153951600-153956800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr1:153951600-153957000	Weak transcription	Brain Angular Gyrus	brain
41	chr1:153951600-153957000	Weak transcription	Hela-S3	cervix
42	chr1:153951600-153958800	Weak transcription	Primary T cells from cord blood	blood
43	chr1:153951800-153956200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:153951800-153957200	Weak transcription	GM12878-XiMat	blood
45	chr1:153951800-153958000	Weak transcription	Dnd41	blood
46	chr1:153952200-153956800	Weak transcription	HepG2	liver
47	chr1:153952400-153956000	Strong transcription	Fetal Intestine Small	intestine
48	chr1:153952400-153956400	Strong transcription	Fetal Stomach	stomach
49	chr1:153952400-153956800	Strong transcription	Osteobl	bone
50	chr1:153952600-153956400	Strong transcription	iPS-15b Cell Line	embryonic stem cell

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