Variant report

Variant	rs3112190
Chromosome Location	chr2:38996561-38996562
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38976319..38979796-chr2:38988969..38996616,16	MCF-7	breast:
2	chr2:38973912..38980240-chr2:38989822..38999883,17	MCF-7	breast:
3	chr2:38977122..38981176-chr2:38994666..38999219,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GALM-4	chr2:38996407-38996666	NONHSAT070198

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10168028	1.00[ASN][1000 genomes]
rs10196452	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10200935	1.00[ASN][1000 genomes]
rs10203173	1.00[ASN][1000 genomes]
rs13015612	1.00[GIH][hapmap]
rs13390845	1.00[ASN][1000 genomes]
rs13393938	1.00[ASN][1000 genomes]
rs13412656	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13418902	1.00[ASN][1000 genomes]
rs13419028	1.00[ASN][1000 genomes]
rs13425948	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541877	1.00[CHD][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs17023076	1.00[ASN][1000 genomes]
rs1897327	1.00[ASN][1000 genomes]
rs3099969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112187	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6746931	0.80[CEU][hapmap];0.88[TSI][hapmap]
rs6753616	1.00[ASN][1000 genomes]
rs6760965	1.00[ASN][1000 genomes]
rs72797312	0.96[EUR][1000 genomes]
rs72797353	1.00[ASN][1000 genomes]
rs72797362	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
4	nsv1014616	chr2:38985472-39022893	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3112190	DHX57	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38979200-39005000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:38993400-38998800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:38993600-38999000	Weak transcription	Osteobl	bone
4	chr2:38993800-38997200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:38994200-38998200	Enhancers	Fetal Heart	heart
6	chr2:38994600-38998800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:38994600-39004600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:38995200-38998800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:38995400-38998800	Weak transcription	HepG2	liver
10	chr2:38995600-38999000	Weak transcription	Liver	Liver
11	chr2:38996400-38999000	Weak transcription	Fetal Intestine Small	intestine

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