Variant report

Variant	rs28900385
Chromosome Location	chr2:234661136-234661137
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	chr2:234651385..234654197-chr2:234659573..234662296,2	MCF-7	breast:
2	chr2:234660399..234662742-chr2:234667989..234670944,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UGT1A1-1	chr2:234660991-234661189	NONHSAT077510

Variant related genes	Relation type
ENSG00000241635	Chromatin interaction
ENSG00000227802	Chromatin interaction
ENSG00000242366	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1054804	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11675168	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11676072	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11679312	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11683974	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11684169	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11689628	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11691824	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11691827	0.95[EUR][1000 genomes]
rs11695770	0.95[EUR][1000 genomes]
rs12471326	1.00[CEU][hapmap]
rs28898586	1.00[YRI][hapmap]
rs28899180	1.00[YRI][hapmap]
rs28899194	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28899468	1.00[YRI][hapmap]
rs28899469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28899472	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28900371	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs28900373	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28900379	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28900384	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34622615	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45449995	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45454101	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45510999	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60103279	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61296714	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6708136	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6740653	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6741543	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv3215	chr2:234631123-234670276	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv1811811	chr2:234633964-234709430	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	esv1810125	chr2:234646637-234662263	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv1809176	chr2:234646637-234664902	Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv1804356	chr2:234648708-234662986	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv1808921	chr2:234648954-234666236	Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv1811500	chr2:234648954-234666236	Bivalent Enhancer Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv2760613	chr2:234650604-234662263	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	esv3413368	chr2:234652296-234663778	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	esv3356788	chr2:234653157-234664730	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	esv3506693	chr2:234653208-234664713	Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	esv3506694	chr2:234653208-234664713	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	esv3410272	chr2:234653209-234664817	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	esv8142	chr2:234653225-234664769	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
18	esv3408179	chr2:234653839-234664180	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
19	nsv876018	chr2:234653938-234666461	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
20	nsv584705	chr2:234658623-234665537	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 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	chr2:234626600-234668400	Weak transcription	NHEK	skin
2	chr2:234646400-234666600	Weak transcription	Stomach Mucosa	stomach
3	chr2:234658200-234664000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:234659800-234661800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:234660000-234666200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr2:234660200-234666400	Weak transcription	Colonic Mucosa	Colon
7	chr2:234660600-234663800	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links