Variant report

Variant	rs3112196
Chromosome Location	chr2:39001918-39001919
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38975148..38982473-chr2:39000165..39007764,21	K562	blood:
2	chr2:38995074..38996747-chr2:39000854..39003003,2	MCF-7	breast:
3	chr2:39000825..39002881-chr2:39004010..39005901,3	MCF-7	breast:
4	chr2:38974922..38979621-chr2:38998984..39003561,8	K562	blood:
5	chr2:39001847..39003662-chr2:39018997..39021441,2	K562	blood:

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000232114	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1010859	0.88[JPT][hapmap]
rs10197412	0.91[CHB][hapmap]
rs10865143	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11898812	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12474770	0.85[ASN][1000 genomes]
rs12618118	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs12621103	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs12991609	0.84[ASN][1000 genomes]
rs13024811	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs1529625	0.91[CHB][hapmap]
rs1979143	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[ASN][1000 genomes]
rs2037875	0.91[CHB][hapmap]
rs3097713	0.87[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs3097714	0.91[CEU][hapmap];0.88[JPT][hapmap]
rs3097716	0.83[ASN][1000 genomes]
rs3099952	0.85[AMR][1000 genomes]
rs3099960	0.83[AMR][1000 genomes]
rs3099961	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099965	0.91[ASN][1000 genomes]
rs3099968	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3099971	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3099975	0.85[ASN][1000 genomes]
rs3099977	0.85[ASN][1000 genomes]
rs3099980	0.89[ASN][1000 genomes]
rs3099990	0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[ASN][1000 genomes]
rs3099992	0.85[ASN][1000 genomes]
rs3100000	1.00[JPT][hapmap]
rs3108666	0.86[ASN][1000 genomes]
rs3112142	0.81[CHB][hapmap];0.80[YRI][hapmap];0.89[ASN][1000 genomes]
rs3112143	0.85[ASN][1000 genomes]
rs3112150	0.89[ASN][1000 genomes]
rs3112152	0.86[ASN][1000 genomes]
rs3112156	0.86[ASN][1000 genomes]
rs3112159	0.88[JPT][hapmap]
rs3112161	0.86[ASN][1000 genomes]
rs3112163	1.00[JPT][hapmap]
rs3112178	0.83[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs3112183	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs3112184	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112186	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112188	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112189	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112191	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112192	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112194	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3112198	0.96[ASN][1000 genomes]
rs3112204	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3134628	0.83[CHB][hapmap];0.86[ASN][1000 genomes]
rs3134629	0.86[ASN][1000 genomes]
rs3134630	0.86[ASN][1000 genomes]
rs3134637	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35387882	0.91[ASN][1000 genomes]
rs3731838	0.91[CHB][hapmap]
rs4670268	0.86[JPT][hapmap]
rs4670892	0.85[ASN][1000 genomes]
rs6544175	0.88[AMR][1000 genomes]
rs6715866	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs6717670	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6746818	0.92[CHB][hapmap]
rs756338	0.89[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

No data

Chromatin state (count:7 , 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	chr2:38994600-39004600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:38999200-39003600	Weak transcription	Placenta	Placenta
4	chr2:38999400-39004600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:38999400-39004600	Weak transcription	A549	lung
6	chr2:39000000-39004800	Weak transcription	Fetal Intestine Small	intestine
7	chr2:39001600-39002200	Enhancers	HepG2	liver

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