Variant report

Variant	rs2815412
Chromosome Location	chr1:93663423-93663424
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	chr1:93657541..93659815-chr1:93661672..93664384,2	K562	blood:
2	chr1:93646297..93647835-chr1:93662191..93664054,2	K562	blood:

Variant related genes	Relation type
ENSG00000122483	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10782958	0.81[EUR][1000 genomes]
rs1081526	0.84[AMR][1000 genomes]
rs10874765	0.81[EUR][1000 genomes]
rs10874767	0.80[EUR][1000 genomes]
rs10874771	0.81[EUR][1000 genomes]
rs11164874	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11164878	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11164882	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11164888	0.80[EUR][1000 genomes]
rs11164889	0.80[EUR][1000 genomes]
rs11164890	0.80[EUR][1000 genomes]
rs11582703	0.81[EUR][1000 genomes]
rs11586323	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12057476	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12064785	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12066315	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12067005	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12070900	0.81[EUR][1000 genomes]
rs12071627	0.81[EUR][1000 genomes]
rs12080715	0.80[EUR][1000 genomes]
rs12085959	0.81[EUR][1000 genomes]
rs12087466	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12088338	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12090723	0.81[EUR][1000 genomes]
rs12094547	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12731675	0.81[EUR][1000 genomes]
rs12731809	0.81[EUR][1000 genomes]
rs1323626	0.84[AMR][1000 genomes]
rs1323628	0.82[AMR][1000 genomes]
rs1414367	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1535698	0.81[EUR][1000 genomes]
rs17131699	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2391227	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2484485	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2749735	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2783492	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2783498	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2783506	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2815408	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2815409	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2815410	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2815411	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2815413	0.92[EUR][1000 genomes]
rs2815414	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36057148	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4573531	0.81[EUR][1000 genomes]
rs485622	0.85[EUR][1000 genomes]
rs504810	0.83[EUR][1000 genomes]
rs505531	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs506556	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs519723	0.84[EUR][1000 genomes]
rs522999	0.92[EUR][1000 genomes]
rs546	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55701931	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs558667	0.80[EUR][1000 genomes]
rs559397	0.81[EUR][1000 genomes]
rs56303209	0.81[EUR][1000 genomes]
rs566743	0.81[EUR][1000 genomes]
rs571212	0.84[EUR][1000 genomes]
rs573056	0.89[EUR][1000 genomes]
rs581825	0.91[EUR][1000 genomes]
rs587754	0.81[EUR][1000 genomes]
rs605759	0.86[EUR][1000 genomes]
rs615416	0.92[EUR][1000 genomes]
rs626714	0.80[EUR][1000 genomes]
rs629153	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs637198	0.80[EUR][1000 genomes]
rs658178	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs658877	0.92[EUR][1000 genomes]
rs661566	0.83[EUR][1000 genomes]
rs662546	0.83[EUR][1000 genomes]
rs6657587	0.80[EUR][1000 genomes]
rs6667701	0.80[EUR][1000 genomes]
rs667680	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs670650	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs671559	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs693872	0.82[EUR][1000 genomes]
rs698926	0.84[AMR][1000 genomes]
rs71510760	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7551635	0.81[EUR][1000 genomes]
rs7555292	0.81[EUR][1000 genomes]
rs771452	0.84[AMR][1000 genomes]
rs771457	0.84[AMR][1000 genomes]
rs771460	0.84[AMR][1000 genomes]
rs771466	0.84[AMR][1000 genomes]
rs771472	0.84[AMR][1000 genomes]
rs771474	0.84[AMR][1000 genomes]
rs771480	0.84[AMR][1000 genomes]
rs797660	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs797669	0.82[EUR][1000 genomes]
rs809515	0.84[EUR][1000 genomes]
rs9432700	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2815412	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs2815412	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs2815412	RP4-717I23.3	cis	Artery Tibial	GTEx
rs2815412	RP4-717I23.3	cis	Thyroid	GTEx
rs2815412	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs2815412	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs2815412	RP4-717I23.3	cis	lung	GTEx
rs2815412	RP4-717I23.3	cis	Stomach	GTEx
rs2815412	RP4-717I23.3	cis	Whole Blood	GTEx
rs2815412	RP4-717I23.3	cis	Artery Aorta	GTEx
rs2815412	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2815412	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs2815412	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs2815412	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93646800-93664600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:93647000-93663600	Weak transcription	Fetal Stomach	stomach
3	chr1:93647000-93664600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:93647000-93688000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:93647000-93688600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:93647000-93756400	Weak transcription	Gastric	stomach
7	chr1:93647200-93664200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:93647200-93664200	Weak transcription	Fetal Intestine Small	intestine
9	chr1:93647200-93664400	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:93647200-93664600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:93647200-93664600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:93647200-93667600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:93647200-93667600	Weak transcription	Adipose Nuclei	Adipose
14	chr1:93647200-93668200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:93647200-93681200	Weak transcription	HUVEC	blood vessel
16	chr1:93647200-93684400	Weak transcription	NH-A	brain
17	chr1:93647200-93685000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:93647200-93707400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:93647200-93757600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:93647400-93664800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:93647400-93667400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr1:93647600-93664400	Weak transcription	NHLF	lung
23	chr1:93647600-93670400	Weak transcription	Liver	Liver
24	chr1:93647600-93706600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:93647800-93665000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr1:93647800-93667800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:93648400-93672200	Weak transcription	A549	lung
28	chr1:93648600-93666000	Weak transcription	NHEK	skin
29	chr1:93649000-93684800	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:93650000-93666000	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:93651000-93684800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr1:93651400-93678000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:93651600-93663600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:93654200-93664000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:93654200-93708400	Weak transcription	Esophagus	oesophagus
36	chr1:93654600-93708000	Weak transcription	Ovary	ovary
37	chr1:93654800-93665800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:93655200-93674000	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:93655400-93664600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:93655600-93665800	Weak transcription	HepG2	liver
41	chr1:93656400-93668000	Weak transcription	Fetal Lung	lung
42	chr1:93656400-93686200	Weak transcription	Aorta	Aorta
43	chr1:93656600-93663600	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr1:93656800-93669000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:93657000-93682000	Strong transcription	Dnd41	blood
46	chr1:93657600-93708400	Weak transcription	Left Ventricle	heart
47	chr1:93658400-93666800	Weak transcription	Brain Germinal Matrix	brain
48	chr1:93658600-93664800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:93658600-93667800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr1:93658600-93667800	Weak transcription	K562	blood

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