Variant report

Variant	rs624604
Chromosome Location	chr1:78642418-78642419
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11162473	1.00[AMR][1000 genomes]
rs11804975	1.00[AMR][1000 genomes]
rs11807141	1.00[AMR][1000 genomes]
rs13375373	1.00[AMR][1000 genomes]
rs13376233	1.00[AMR][1000 genomes]
rs1780051	1.00[AMR][1000 genomes]
rs4245659	1.00[AMR][1000 genomes]
rs584562	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs591448	0.82[YRI][hapmap]
rs617905	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs628002	1.00[AMR][1000 genomes]
rs632675	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs633580	0.83[YRI][hapmap]
rs638728	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs645920	1.00[AMR][1000 genomes]
rs662593	1.00[AMR][1000 genomes]
rs663628	1.00[AMR][1000 genomes]
rs9324167	1.00[AMR][1000 genomes]
rs9324168	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1850497	chr1:78596312-78645701	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1000388	chr1:78638946-78665285	Enhancers Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
6	nsv520237	chr1:78639244-78660123	Enhancers Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78625200-78644400	Weak transcription	Pancreas	Pancrea
2	chr1:78635000-78646200	Weak transcription	Fetal Intestine Small	intestine
3	chr1:78641600-78642800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:78641600-78642800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:78641600-78643400	Enhancers	Fetal Muscle Leg	muscle
6	chr1:78641600-78643800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:78641800-78642600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:78641800-78642600	Enhancers	HMEC	breast
9	chr1:78641800-78642600	Enhancers	NHEK	skin
10	chr1:78641800-78642800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:78641800-78643200	Enhancers	Osteobl	bone
12	chr1:78641800-78643800	Enhancers	NHDF-Ad	bronchial
13	chr1:78641800-78645200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:78642000-78642600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr1:78642000-78642600	Enhancers	Stomach Smooth Muscle	stomach
16	chr1:78642000-78643200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:78642000-78643400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:78642000-78643800	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr1:78642200-78642600	Enhancers	HSMMtube	muscle

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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