Variant report

Variant	rs2949646
Chromosome Location	chr4:107288449-107288450
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr4:107288417-107288562	MCF10A-Er-Src	breast:	n/a	chr4:107288500-107288511
2	ZNF143	chr4:107288419-107288563	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr4:107288271-107288509	Gliobla	brain:	n/a	n/a

Variant related genes	Relation type
GIMD1	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11938792	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2691805	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2949626	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2949645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2949647	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3018059	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3018060	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3018061	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3018062	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3018063	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3018064	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3018065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3109959	0.89[CEU][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830029	chr4:107203096-107353483	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1008963	chr4:107282656-107384924	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2949646	OSTC	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:107270800-107290600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr4:107285200-107288600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:107286200-107288800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:107287200-107290600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:107287400-107288600	Enhancers	NHDF-Ad	bronchial
6	chr4:107287400-107290600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr4:107287400-107290800	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr4:107287600-107288800	Enhancers	NH-A	brain
9	chr4:107287600-107290600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:107287800-107290400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr4:107287800-107290400	Weak transcription	HUVEC	blood vessel
12	chr4:107287800-107290600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:107287800-107290600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:107287800-107290600	Weak transcription	Osteobl	bone
15	chr4:107287800-107290800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:107288000-107288600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:107288200-107288600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:107288400-107288800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr4:107288400-107290400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:107288400-107290600	Weak transcription	HSMM	muscle

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