Variant report

Variant	rs7038501
Chromosome Location	chr9:116670142-116670143
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116666574..116671426-chr9:116673853..116679155,7	K562	blood:
2	chr9:116663867..116665785-chr9:116668142..116670914,2	K562	blood:
3	chr9:116646366..116648673-chr9:116669994..116672714,2	K562	blood:
4	chr9:116669450..116672733-chr9:116675778..116678171,3	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10119978	0.80[GIH][hapmap]
rs10120883	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10122390	0.85[CEU][hapmap]
rs10513222	0.96[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs10739396	0.87[GIH][hapmap]
rs10817531	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10817532	0.85[CEU][hapmap]
rs10817535	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10817541	0.89[GIH][hapmap]
rs10982007	0.96[CEU][hapmap]
rs10982017	0.80[GIH][hapmap]
rs1330166	0.89[YRI][hapmap]
rs1330169	0.96[CEU][hapmap]
rs1544102	0.82[GIH][hapmap]
rs2065184	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2150014	0.89[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2183364	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2418259	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs2418260	0.84[GIH][hapmap]
rs2900569	0.85[CEU][hapmap]
rs2900570	0.84[GIH][hapmap]
rs2900571	0.89[YRI][hapmap]
rs35381898	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4979294	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979297	0.85[CEU][hapmap]
rs4979298	0.96[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6478045	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6478046	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6478047	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7026176	0.89[CEU][hapmap]
rs7029830	0.85[CEU][hapmap]
rs7047895	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs7852787	0.85[CEU][hapmap]
rs7853127	0.85[CEU][hapmap]
rs7855811	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7870363	0.89[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs814680	0.80[GIH][hapmap]
rs882980	0.96[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs944180	0.96[CEU][hapmap]
rs9942975	0.96[CEU][hapmap];0.93[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7038501	SLC46A2	cis	parietal	SCAN
rs7038501	PALM2-AKAP2	cis	parietal	SCAN
rs7038501	MUSK	cis	parietal	SCAN
rs7038501	ZNF618	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116651200-116675000	Weak transcription	Colon Smooth Muscle	Colon
2	chr9:116653200-116671800	Weak transcription	Fetal Lung	lung
3	chr9:116653800-116674000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:116659400-116685400	Weak transcription	A549	lung
5	chr9:116662000-116671400	Weak transcription	Right Ventricle	heart
6	chr9:116664000-116674400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:116666400-116683800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr9:116666600-116683000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:116667200-116674200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr9:116667400-116684400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr9:116667800-116673200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr9:116668000-116671400	Enhancers	Fetal Thymus	thymus
13	chr9:116668000-116681800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:116668400-116670200	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr9:116668400-116670600	Enhancers	H1 Cell Line	embryonic stem cell
16	chr9:116668600-116670200	Enhancers	Stomach Mucosa	stomach
17	chr9:116668600-116672600	Enhancers	Pancreas	Pancrea
18	chr9:116668800-116678800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr9:116669000-116670200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr9:116669000-116670200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:116669000-116670200	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr9:116669000-116670400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:116669200-116670200	Strong transcription	Fetal Stomach	stomach
24	chr9:116669200-116670200	Enhancers	HMEC	breast
25	chr9:116669400-116671400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr9:116669400-116674400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:116669400-116675000	Weak transcription	Adipose Nuclei	Adipose
28	chr9:116669400-116675400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:116669400-116675400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:116669400-116683000	Weak transcription	Osteobl	bone
31	chr9:116669600-116670400	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr9:116669600-116670400	Strong transcription	Fetal Intestine Small	intestine
33	chr9:116669600-116674200	Weak transcription	NHLF	lung
34	chr9:116669600-116674400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr9:116669600-116674400	Weak transcription	Aorta	Aorta
36	chr9:116669600-116674400	Weak transcription	Brain Anterior Caudate	brain
37	chr9:116669600-116675000	Weak transcription	NHDF-Ad	bronchial
38	chr9:116669600-116690400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr9:116669800-116670600	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr9:116669800-116670800	Weak transcription	Ovary	ovary
41	chr9:116669800-116671800	Weak transcription	Liver	Liver
42	chr9:116669800-116672400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:116669800-116673600	Weak transcription	Fetal Muscle Leg	muscle
44	chr9:116669800-116674200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:116669800-116674200	Weak transcription	NHEK	skin
46	chr9:116669800-116674400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr9:116669800-116674400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr9:116669800-116674400	Weak transcription	HSMM	muscle
49	chr9:116669800-116675400	Weak transcription	Right Atrium	heart
50	chr9:116669800-116683600	Weak transcription	HUVEC	blood vessel

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