Variant report

Variant	rs12130499
Chromosome Location	chr1:224836514-224836515
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10799277	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs10799590	1.00[CEU][hapmap];0.81[CHD][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10915684	0.95[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10915694	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs10915696	0.95[CEU][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs10915698	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs10915699	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs12092438	0.93[EUR][1000 genomes]
rs12121558	0.87[CEU][hapmap]
rs12124262	1.00[CEU][hapmap];0.94[CHB][hapmap]
rs12132665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13374487	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs1369847	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1436169	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1436171	0.80[CEU][hapmap];0.87[EUR][1000 genomes]
rs1436172	0.95[CEU][hapmap]
rs1465768	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs1603917	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1603918	1.00[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs169888	0.95[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1965777	0.86[EUR][1000 genomes]
rs2405525	0.86[EUR][1000 genomes]
rs2648746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2897161	0.88[EUR][1000 genomes]
rs2936575	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs298732	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs298733	0.95[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs298734	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs298735	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs298738	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs298739	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2993124	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3012185	0.95[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4147293	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653402	0.95[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4653404	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4653591	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4653592	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56881651	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs61676104	0.86[EUR][1000 genomes]
rs6667034	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6686604	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs6686633	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs67817586	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs713098	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7511897	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs7521396	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7535296	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7537973	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7542431	0.82[EUR][1000 genomes]
rs7542995	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs7543218	0.92[EUR][1000 genomes]
rs7544312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7545574	0.95[CEU][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs873594	0.80[CEU][hapmap];0.87[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	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12130499	RAB3GAP2	cis	cerebellum	SCAN
rs12130499	DEGS1	cis	cerebellum	SCAN
rs12130499	MARK1	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224820400-224840000	Weak transcription	Right Atrium	heart
2	chr1:224826000-224839200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:224826400-224837800	Weak transcription	NHLF	lung
4	chr1:224827000-224839800	Weak transcription	HSMM	muscle
5	chr1:224828600-224837800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:224828800-224853400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:224832200-224839800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:224832200-224884400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:224832800-224837600	Weak transcription	Ovary	ovary
10	chr1:224832800-224838000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:224832800-224869000	Weak transcription	Dnd41	blood
12	chr1:224833200-224874400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:224833400-224840600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:224833600-224837600	Weak transcription	NHDF-Ad	bronchial
15	chr1:224835400-224837600	Weak transcription	Fetal Brain Male	brain
16	chr1:224835600-224836600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:224835600-224837800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:224835600-224837800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:224835600-224838000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:224835600-224838000	Weak transcription	NH-A	brain
21	chr1:224835600-224839800	Weak transcription	Pancreas	Pancrea
22	chr1:224836000-224837000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:224836000-224840200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links