Variant report

Variant	rs57407575
Chromosome Location	chr1:174084642-174084643
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174084142..174085721-chr1:174085746..174087770,2	K562	blood:
2	chr1:174082792..174085808-chr1:174127455..174130130,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RC3H1-1	chr1:174084521-174084787	ENSG00000227373
2	lnc-RC3H1-1	chr1:174084438-174084787	ENSG00000227373
3	lnc-RC3H1-1	chr1:174083921-174084787	NONHSAT007722

Variant related genes	Relation type
ENSG00000227373	Chromatin interaction
ENSG00000152061	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10798307	0.81[EUR][1000 genomes]
rs10912728	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912733	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912735	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912737	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912740	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912741	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912746	0.82[EUR][1000 genomes]
rs10912747	0.82[EUR][1000 genomes]
rs10912750	0.82[EUR][1000 genomes]
rs10912754	0.81[EUR][1000 genomes]
rs11802158	0.82[EUR][1000 genomes]
rs11807537	0.80[EUR][1000 genomes]
rs12065785	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12075630	0.92[ASN][1000 genomes]
rs12076453	0.82[EUR][1000 genomes]
rs12076771	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12079214	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079687	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079689	0.82[EUR][1000 genomes]
rs12080977	0.82[EUR][1000 genomes]
rs12081445	0.82[EUR][1000 genomes]
rs12082461	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12085311	0.82[EUR][1000 genomes]
rs12087808	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091157	0.81[EUR][1000 genomes]
rs12093691	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12354141	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1407127	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1417186	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846717	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846718	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846816	0.82[EUR][1000 genomes]
rs17300775	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17350956	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17350991	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17353198	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1934681	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2103640	0.82[EUR][1000 genomes]
rs2860907	0.82[EUR][1000 genomes]
rs3086	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233169	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4607949	0.82[EUR][1000 genomes]
rs4650950	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650951	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650958	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650959	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650968	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4650969	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4650981	0.82[EUR][1000 genomes]
rs4652179	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4652191	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652193	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652204	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652275	0.81[EUR][1000 genomes]
rs55698100	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56152378	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56158362	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56239105	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56338048	0.82[EUR][1000 genomes]
rs56375942	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56404641	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59044210	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6656491	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666588	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6668008	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670425	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676161	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685499	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692437	0.82[EUR][1000 genomes]
rs6694208	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724888	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724889	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711443	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72711448	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72711457	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711487	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711492	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711501	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72713503	0.82[EUR][1000 genomes]
rs72713504	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72713505	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs727912	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535987	0.82[EUR][1000 genomes]
rs7551605	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831937	chr1:173949373-174131463	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv465661	chr1:174014507-174152688	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv548193	chr1:174014507-174152688	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv1008314	chr1:174080192-174311023	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv535207	chr1:174080192-174311023	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs57407575	RABGAP1L	cis	Esophagus Muscularis	GTEx
rs57407575	RP11-160H22.5	cis	Thyroid	GTEx
rs57407575	MRPS14	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174081800-174086200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:174083600-174084800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:174084000-174085000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:174084000-174085200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:174084000-174085200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr1:174084200-174084800	Enhancers	Fetal Intestine Small	intestine
7	chr1:174084200-174085400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:174084200-174085600	Enhancers	Hela-S3	cervix
9	chr1:174084600-174085600	Enhancers	HepG2	liver
10	chr1:174084600-174088000	Weak transcription	Fetal Heart	heart

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