Variant report

Variant	rs61887473
Chromosome Location	chr1:196664728-196664729
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10501127	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11599935	1.00[ASN][1000 genomes]
rs11607549	1.00[ASN][1000 genomes]
rs12420580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1522086	1.00[ASN][1000 genomes]
rs17760306	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17760694	1.00[ASN][1000 genomes]
rs2273121	1.00[ASN][1000 genomes]
rs3181268	1.00[ASN][1000 genomes]
rs3181269	1.00[ASN][1000 genomes]
rs56026019	1.00[ASN][1000 genomes]
rs61887474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61887477	1.00[ASN][1000 genomes]
rs7930105	1.00[ASN][1000 genomes]
rs7941387	1.00[ASN][1000 genomes]
rs7943459	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931415	chr1:196270759-196744780	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv2757766	chr1:196590837-196961802	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv428290	chr1:196590837-196961802	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	esv2758990	chr1:196590837-197169772	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv427897	chr1:196590837-197169772	Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv428565	chr1:196604434-196772489	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv1010642	chr1:196629637-196874948	Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv535258	chr1:196629637-196874948	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
10	nsv872962	chr1:196632470-196692659	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv872965	chr1:196642233-196779888	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
12	nsv872968	chr1:196652622-196685671	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv872971	chr1:196656271-196712257	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv872972	chr1:196656670-196684855	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
15	nsv872975	chr1:196656737-196670757	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
16	nsv872977	chr1:196657064-196670757	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
17	nsv872979	chr1:196658279-196670757	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
18	nsv1001720	chr1:196658295-196944678	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
19	nsv535259	chr1:196658295-196944678	Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
20	nsv872980	chr1:196658763-196670757	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
21	nsv548747	chr1:196659178-196670757	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Genic enhancers	n/a	n/a	inside rSNPs	n/a
22	nsv947215	chr1:196661520-196683517	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61887473	CD59	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196628800-196679400	Weak transcription	Psoas Muscle	Psoas
2	chr1:196629200-196672600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:196639800-196670400	Weak transcription	Adipose Nuclei	Adipose
4	chr1:196640000-196676800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:196641400-196665800	Strong transcription	Liver	Liver
6	chr1:196642000-196675200	Weak transcription	Fetal Stomach	stomach
7	chr1:196646000-196678400	Weak transcription	K562	blood
8	chr1:196648200-196666600	Weak transcription	NH-A	brain
9	chr1:196648200-196670200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:196648400-196706200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:196649600-196707200	Weak transcription	Osteobl	bone
12	chr1:196653600-196673600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:196653800-196669600	Weak transcription	Lung	lung
14	chr1:196655000-196671600	Weak transcription	Esophagus	oesophagus
15	chr1:196655200-196672200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr1:196659600-196670400	Weak transcription	HSMM	muscle
17	chr1:196660000-196692600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:196660200-196669400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:196660400-196667400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:196662600-196665600	Strong transcription	Dnd41	blood
21	chr1:196662600-196665800	Strong transcription	Ovary	ovary
22	chr1:196663000-196665200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr1:196663600-196665200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:196663800-196669200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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