Variant report

Variant	rs2378910
Chromosome Location	chr1:185232251-185232252
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:185230521..185233061-chr1:185233311..185235376,2	MCF-7	breast:
2	chr1:185231859..185233579-chr1:185234900..185236407,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233583	Chromatin interaction
ENSG00000252612	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10157232	0.81[EUR][1000 genomes]
rs10174	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10752947	0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs10798002	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10798003	1.00[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs10798004	0.82[EUR][1000 genomes]
rs10798006	0.81[EUR][1000 genomes]
rs10911693	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10911700	1.00[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs10911702	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10911704	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10911708	0.87[EUR][1000 genomes]
rs12026391	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12041704	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12044943	0.81[EUR][1000 genomes]
rs12118722	0.82[ASN][1000 genomes]
rs12120377	0.84[ASN][1000 genomes]
rs12135769	0.96[CEU][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs12136040	0.97[EUR][1000 genomes]
rs1336752	0.84[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1336753	0.92[EUR][1000 genomes]
rs17641003	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1889976	1.00[CEU][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs2095610	0.91[EUR][1000 genomes]
rs2152707	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2224027	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs2281416	0.83[CHB][hapmap]
rs2378909	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34611062	0.96[EUR][1000 genomes]
rs57977436	0.96[EUR][1000 genomes]
rs6656019	0.82[EUR][1000 genomes]
rs6682891	0.81[EUR][1000 genomes]
rs66845254	0.82[EUR][1000 genomes]
rs6685627	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6687774	0.83[CHB][hapmap]
rs7123	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs726567	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7512337	0.81[EUR][1000 genomes]
rs7535064	0.84[ASN][1000 genomes]
rs7535261	0.81[ASN][1000 genomes]
rs7537341	0.89[CEU][hapmap];0.88[MEX][hapmap];0.81[EUR][1000 genomes]
rs7539575	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7542721	0.98[EUR][1000 genomes]
rs7545878	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs7550586	0.84[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs883753	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951428	0.84[CHB][hapmap];0.92[CHD][hapmap];0.95[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	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv548398	chr1:185136458-186003094	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2378910	RNF2	cis	multi-tissue	Pritchard
rs2378910	RP4-635A23.4	cis	Artery Tibial	GTEx
rs2378910	IVNS1ABP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185193800-185263600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:185210600-185250400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:185218800-185269400	Weak transcription	Pancreas	Pancrea
4	chr1:185227000-185247400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:185227800-185262000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:185228800-185250400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:185229800-185232800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:185230400-185247000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:185230600-185233000	Weak transcription	Fetal Heart	heart
10	chr1:185230600-185236200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:185231000-185263400	Weak transcription	Fetal Kidney	kidney
12	chr1:185231800-185232600	Enhancers	K562	blood
13	chr1:185231800-185234400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:185231800-185249200	Weak transcription	Primary T cells from cord blood	blood

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