Variant report

Variant	rs4723979
Chromosome Location	chr7:40868141-40868142
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1013574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10233069	0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs10235458	0.82[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs10247275	1.00[CEU][hapmap];0.81[JPT][hapmap];0.99[EUR][1000 genomes]
rs10279715	0.87[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs1029621	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs12537964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538907	0.82[AFR][1000 genomes]
rs12538933	0.80[MKK][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs12538949	0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs12538965	0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs13243593	0.82[ASN][1000 genomes]
rs13246232	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1921757	0.87[LWK][hapmap];0.80[YRI][hapmap]
rs2108375	0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs2108376	0.84[ASN][1000 genomes]
rs34565813	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34689844	0.84[ASN][1000 genomes]
rs6462989	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6949092	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809981	0.80[YRI][hapmap];0.84[AFR][1000 genomes]
rs9639838	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030648	chr7:40218618-41032599	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830972	chr7:40814709-40945917	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv1827128	chr7:40862370-40886576	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4723979	GPR141	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40862200-40868200	Enhancers	HMEC	breast
2	chr7:40864000-40869000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr7:40864000-40869600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr7:40864000-40871000	Enhancers	NHDF-Ad	bronchial
5	chr7:40865400-40868200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:40865600-40868600	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr7:40866000-40868400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr7:40866000-40868600	Enhancers	Adipose Nuclei	Adipose
9	chr7:40866600-40868600	Enhancers	Stomach Smooth Muscle	stomach
10	chr7:40867000-40872400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr7:40867200-40868800	Enhancers	HSMMtube	muscle
12	chr7:40867200-40868800	Enhancers	Osteobl	bone
13	chr7:40867200-40869200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:40867200-40870000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr7:40867400-40871400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr7:40867400-40872200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr7:40867400-40872400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr7:40867600-40868200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr7:40867600-40868600	Weak transcription	Fetal Stomach	stomach
20	chr7:40867600-40869600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:40867600-40869600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:40867600-40869800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr7:40867600-40869800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr7:40867600-40872600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr7:40867600-40872600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr7:40867600-40873000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr7:40867600-40882600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:40867800-40868200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr7:40867800-40873000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr7:40867800-40875800	Weak transcription	NHEK	skin
31	chr7:40867800-40877200	Weak transcription	HSMM	muscle
32	chr7:40868000-40868600	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr7:40868000-40869600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr7:40868000-40870800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr7:40868000-40871000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr7:40868000-40871600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr7:40868000-40873400	Weak transcription	Aorta	Aorta

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