Variant report

Variant	rs1635544
Chromosome Location	chr12:48380031-48380032
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	BHLHE40	chr12:48379961-48380049	K562	blood:	n/a	n/a

Variant related genes	Relation type
COL2A1	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11168337	0.88[CEU][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12721428	0.86[JPT][hapmap]
rs1621710	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1635534	0.87[ASN][1000 genomes]
rs1635535	0.87[ASN][1000 genomes]
rs1635536	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1635537	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1635546	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1635547	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1635550	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs1635553	0.92[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1793911	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1793912	0.86[ASN][1000 genomes]
rs1793913	0.86[ASN][1000 genomes]
rs1793915	0.85[ASN][1000 genomes]
rs1793917	0.82[ASN][1000 genomes]
rs1793923	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1793924	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1793937	0.82[JPT][hapmap]
rs1793949	0.82[JPT][hapmap]
rs2070739	0.86[JPT][hapmap]
rs2276454	0.82[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs2276455	0.83[AMR][1000 genomes]
rs2276456	0.82[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap]
rs3829734	0.91[ASN][1000 genomes]
rs3829736	0.88[CEU][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs740024	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs917055	0.88[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]

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	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv899061	chr12:48360620-48389023	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv519659	chr12:48366449-48389245	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1635544	C12orf68	cis	parietal	SCAN
rs1635544	PRPF40B	cis	parietal	SCAN
rs1635544	LMBR1L	cis	cerebellum	SCAN
rs1635544	ASB8	cis	cerebellum	SCAN
rs1635544	FAM186B	cis	cerebellum	SCAN
rs1635544	PROCA1	trans	cerebellum	SCAN
rs1635544	SNORA2A	cis	parietal	SCAN
rs1635544	PRICKLE1	cis	parietal	SCAN
rs1635544	PRKAG1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48358600-48381400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:48359200-48384000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:48363400-48383000	Weak transcription	Spleen	Spleen
4	chr12:48364400-48381200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:48365200-48381600	Weak transcription	Right Atrium	heart
6	chr12:48365400-48381000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:48366200-48381200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:48366200-48381400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:48366200-48381600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:48375000-48381600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:48375200-48381200	Weak transcription	Fetal Muscle Leg	muscle
12	chr12:48376400-48380800	Strong transcription	Fetal Intestine Small	intestine
13	chr12:48376800-48391000	Weak transcription	Fetal Intestine Large	intestine
14	chr12:48378400-48381400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:48379000-48380800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:48379400-48382000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:48380000-48380800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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