Variant report

Variant	rs2104500
Chromosome Location	chr1:153477813-153477814
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr1:153477603-153477833	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153475901..153479398-chr1:153483925..153488105,4	K562	blood:
2	chr1:153477007..153479814-chr1:153598279..153601276,3	MCF-7	breast:
3	chr1:153476869..153479043-chr1:153480773..153483334,2	K562	blood:
4	chr1:153320974..153341807-chr1:153456098..153486349,81	MCF-7	breast:

Variant related genes	Relation type
RN7SL44P	TF binding region
ENSG00000163218	Chromatin interaction
ENSG00000163220	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000160678	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11488667	1.00[EUR][1000 genomes]
rs11973	1.00[EUR][1000 genomes]
rs16835357	1.00[EUR][1000 genomes]
rs16835362	1.00[EUR][1000 genomes]
rs16835371	1.00[EUR][1000 genomes]
rs16835373	1.00[EUR][1000 genomes]
rs16835375	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16835379	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16835389	1.00[EUR][1000 genomes]
rs16835409	1.00[EUR][1000 genomes]
rs16835413	1.00[EUR][1000 genomes]
rs16835417	1.00[EUR][1000 genomes]
rs2230870	1.00[EUR][1000 genomes]
rs28373144	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28407716	1.00[EUR][1000 genomes]
rs28442251	1.00[EUR][1000 genomes]
rs28451322	1.00[EUR][1000 genomes]
rs28456342	1.00[EUR][1000 genomes]
rs28485860	1.00[EUR][1000 genomes]
rs28510499	1.00[EUR][1000 genomes]
rs28578863	1.00[EUR][1000 genomes]
rs28587171	1.00[EUR][1000 genomes]
rs28605603	1.00[EUR][1000 genomes]
rs28634320	1.00[EUR][1000 genomes]
rs28645589	1.00[EUR][1000 genomes]
rs28648662	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28690872	1.00[EUR][1000 genomes]
rs28694652	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28709866	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28784102	1.00[EUR][1000 genomes]
rs3014827	1.00[EUR][1000 genomes]
rs3856025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56140059	1.00[EUR][1000 genomes]
rs56255753	1.00[EUR][1000 genomes]
rs56401460	1.00[EUR][1000 genomes]
rs58529054	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59209384	1.00[EUR][1000 genomes]
rs59617976	1.00[EUR][1000 genomes]
rs60219287	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60460123	1.00[EUR][1000 genomes]
rs61038462	1.00[EUR][1000 genomes]
rs61131911	1.00[EUR][1000 genomes]
rs61148582	1.00[EUR][1000 genomes]
rs73009954	1.00[EUR][1000 genomes]
rs73011738	1.00[EUR][1000 genomes]
rs73020460	1.00[EUR][1000 genomes]
rs73020461	1.00[EUR][1000 genomes]
rs73020464	1.00[EUR][1000 genomes]
rs73020467	1.00[EUR][1000 genomes]
rs73020468	1.00[EUR][1000 genomes]
rs73020471	1.00[EUR][1000 genomes]
rs73020473	1.00[EUR][1000 genomes]
rs73020474	1.00[EUR][1000 genomes]
rs73020478	1.00[EUR][1000 genomes]
rs73020479	1.00[EUR][1000 genomes]
rs73020496	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73020497	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73024502	1.00[EUR][1000 genomes]
rs73026308	1.00[EUR][1000 genomes]
rs730347	1.00[EUR][1000 genomes]
rs74115477	1.00[EUR][1000 genomes]
rs74115478	1.00[EUR][1000 genomes]
rs74115489	1.00[EUR][1000 genomes]
rs746425	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7518794	1.00[EUR][1000 genomes]
rs7528738	1.00[EUR][1000 genomes]
rs7543851	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153462800-153479000	Weak transcription	Right Atrium	heart
2	chr1:153467200-153478000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:153468400-153479000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:153471800-153478800	Weak transcription	Fetal Stomach	stomach
5	chr1:153472400-153478200	Weak transcription	Aorta	Aorta
6	chr1:153474400-153478400	Weak transcription	Fetal Lung	lung
7	chr1:153475400-153478800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:153476000-153478000	Weak transcription	HSMM	muscle
9	chr1:153476600-153478800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:153477000-153478800	Weak transcription	HMEC	breast
11	chr1:153477200-153478800	Weak transcription	NHEK	skin
12	chr1:153477800-153479000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:153477800-153479600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:153477800-153480400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:153477800-153480800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:153477800-153480800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr1:153477800-153481000	Enhancers	Fetal Muscle Leg	muscle
18	chr1:153477800-153481200	Enhancers	Ovary	ovary

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