Variant report

Variant	rs61852483
Chromosome Location	chr1:246908816-246908817
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10924821	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12117138	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12123234	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12124249	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12129922	1.00[AMR][1000 genomes]
rs12136007	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12143299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12144608	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12737081	0.96[AFR][1000 genomes]
rs12741733	0.96[AFR][1000 genomes]
rs34116211	0.84[AFR][1000 genomes]
rs57538659	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61852473	1.00[AMR][1000 genomes]
rs61852486	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61852487	0.92[EUR][1000 genomes]
rs61852488	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61852489	0.92[EUR][1000 genomes]
rs61852490	0.92[EUR][1000 genomes]
rs61852513	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61852517	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6665017	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6676751	0.92[EUR][1000 genomes]
rs74154805	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers 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	52 gene(s)	inside rSNPs	diseases
6	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS 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	16 gene(s)	inside rSNPs	diseases
7	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv870294	chr1:246877043-246927940	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1006262	chr1:246892826-246964775	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv523531	chr1:246893948-246967899	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS 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	14 gene(s)	inside rSNPs	diseases
12	nsv999756	chr1:246894542-246969660	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61852483	RP11-439E19.10	cis	Muscle Skeletal	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
2	chr1:246888600-246945600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:246889000-246929000	Weak transcription	Stomach Mucosa	stomach
4	chr1:246890200-246913200	Strong transcription	Fetal Muscle Leg	muscle
5	chr1:246890400-246909000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:246890600-246914000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:246891800-246911600	Strong transcription	Liver	Liver
8	chr1:246892400-246912000	Strong transcription	Dnd41	blood
9	chr1:246892600-246909200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:246892600-246924400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:246893800-246912800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:246894400-246909600	Strong transcription	Placenta	Placenta
13	chr1:246894600-246923800	Weak transcription	Pancreas	Pancrea
14	chr1:246895000-246909000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:246895000-246909200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr1:246895000-246912000	Weak transcription	Spleen	Spleen
17	chr1:246895000-246942200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr1:246895400-246938600	Weak transcription	Fetal Heart	heart
19	chr1:246896400-246917000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:246897400-246909000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:246897400-246909200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:246897600-246909200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:246897600-246912400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:246900000-246917600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:246900400-246910400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:246900800-246912200	Weak transcription	Esophagus	oesophagus
27	chr1:246901200-246924000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:246902000-246909000	Strong transcription	HSMMtube	muscle
29	chr1:246902200-246909000	Strong transcription	NHDF-Ad	bronchial
30	chr1:246902400-246909000	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:246902600-246912200	Weak transcription	Lung	lung
32	chr1:246902800-246923200	Weak transcription	Fetal Brain Male	brain
33	chr1:246902800-246923800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr1:246902800-246952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:246903000-246909200	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:246903000-246917200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:246904000-246909000	Strong transcription	Fetal Thymus	thymus
38	chr1:246904400-246909000	Strong transcription	A549	lung
39	chr1:246904400-246911400	Weak transcription	Fetal Lung	lung
40	chr1:246904600-246942800	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr1:246905000-246909000	Strong transcription	Fetal Brain Female	brain
42	chr1:246905000-246909200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:246905000-246910800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:246905000-246911600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr1:246905000-246922200	Weak transcription	Brain Germinal Matrix	brain
46	chr1:246905000-246922200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr1:246905000-246923600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:246905000-246923800	Weak transcription	Thymus	Thymus
49	chr1:246905000-246924000	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr1:246905000-246945800	Weak transcription	Psoas Muscle	Psoas

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