Variant report

Variant	rs5015340
Chromosome Location	chr1:45986269-45986270
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:36)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:36 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45804762..45807081-chr1:45985847..45987732,3	K562	blood:
2	chr1:45984510..45988941-chr1:46031540..46035902,8	MCF-7	breast:
3	chr1:45973182..45975128-chr1:45984664..45989019,3	MCF-7	breast:
4	chr1:45985173..45987673-chr1:46047489..46052049,5	MCF-7	breast:
5	chr1:45184712..45189957-chr1:45986029..45989344,7	K562	blood:
6	chr1:45985920..45989261-chr1:46150872..46154561,4	K562	blood:
7	chr1:45982342..45989534-chr1:46006947..46020678,57	K562	blood:
8	chr1:45186094..45189073-chr1:45986029..45988855,6	K562	blood:
9	chr1:45975860..45989626-chr1:46030076..46041078,36	K562	blood:
10	chr1:45985760..45988673-chr3:181223417..181224917,2	K562	blood:
11	chr1:45283995..45285689-chr1:45985443..45988306,2	K562	blood:
12	chr1:45976870..45989534-chr1:46007918..46019226,54	K562	blood:
13	chr1:45984465..45989261-chr1:46150683..46156386,7	K562	blood:
14	chr1:45985569..45992282-chr1:46014173..46025125,38	MCF-7	breast:
15	chr1:45985928..45987580-chr1:46638994..46641452,2	K562	blood:
16	chr1:45805652..45808329-chr1:45985496..45987569,2	K562	blood:
17	chr1:45982844..45990993-chr1:46030121..46038313,25	K562	blood:
18	chr1:45980210..45995142-chr1:46046095..46057139,89	K562	blood:
19	chr1:45974558..45995867-chr1:46046173..46057010,94	K562	blood:
20	chr1:45986006..45987608-chr1:46151069..46153462,2	MCF-7	breast:
21	chr1:45476976..45478536-chr1:45986194..45987782,2	K562	blood:
22	chr1:45986151..45989227-chr1:46047437..46050636,3	MCF-7	breast:
23	chr1:45476953..45479637-chr1:45985604..45989189,5	K562	blood:
24	chr1:45239811..45242258-chr1:45985710..45988896,3	K562	blood:
25	chr1:43291298..43293447-chr1:45985281..45987482,2	K562	blood:
26	chr1:45770153..45772059-chr1:45985117..45987576,2	K562	blood:
27	chr1:45985928..45987580-chr1:46638994..46641452,3	K562	blood:
28	chr1:45985941..45987722-chr17:59477306..59479148,2	MCF-7	breast:
29	chr1:45985342..45989391-chr1:46011113..46019467,18	MCF-7	breast:
30	chr1:45985980..45988948-chr1:46213742..46217743,4	K562	blood:
31	chr1:45982735..45988890-chr1:46031987..46038228,10	MCF-7	breast:
32	chr1:45956512..45959436-chr1:45986078..45988665,3	MCF-7	breast:
33	chr1:45307699..45310286-chr1:45986112..45988725,2	K562	blood:
34	chr1:45195127..45198642-chr1:45986086..45989017,4	K562	blood:
35	chr1:45969960..45972308-chr1:45985412..45987180,2	MCF-7	breast:
36	chr1:45984572..45987422-chr1:46019368..46021467,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000159592	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000070759	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000159596	Chromatin interaction
ENSG00000197429	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000235294	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000162415	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000117472	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000226499	Chromatin interaction
ENSG00000126107	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1006216	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1007858	0.82[AMR][1000 genomes]
rs10789464	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10890330	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11211111	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11211117	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11211118	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11211123	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11211124	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211128	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11211137	0.82[EUR][1000 genomes]
rs11211139	0.83[EUR][1000 genomes]
rs12029322	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12037201	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12042903	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12049503	0.82[EUR][1000 genomes]
rs12066142	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12067642	0.87[EUR][1000 genomes]
rs12077621	0.83[EUR][1000 genomes]
rs12564806	0.85[EUR][1000 genomes]
rs2055145	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28555082	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2883968	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34673142	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34768551	0.83[EUR][1000 genomes]
rs3790583	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4633317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4660858	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4660863	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55642258	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61788281	0.81[EUR][1000 genomes]
rs61788285	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61788336	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61788356	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67683090	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs713358	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7528573	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs868351	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9727262	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9729395	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
5	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
6	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
7	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
8	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5015340	C2orf49	trans	lymphoblastoid	RTeQTL
rs5015340	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs5015340	TESK2	cis	Whole Blood	GTEx
rs5015340	PRDX1	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45983200-45986400	Weak transcription	Pancreas	Pancrea
2	chr1:45984400-45986400	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chr1:45984600-45987000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:45985200-45986400	Weak transcription	Small Intestine	intestine
5	chr1:45985200-45987000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:45985200-45987800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:45985200-45987800	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr1:45985200-45987800	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr1:45985200-45987800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:45985200-45987800	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr1:45985200-45987800	Active TSS	Colon Smooth Muscle	Colon
12	chr1:45985200-45987800	Active TSS	HSMMtube	muscle
13	chr1:45985200-45988000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:45985200-45988000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:45985200-45988000	Active TSS	Brain Anterior Caudate	brain
16	chr1:45985200-45988000	Active TSS	Brain Substantia Nigra	brain
17	chr1:45985200-45988200	Active TSS	NHLF	lung
18	chr1:45985200-45988400	Active TSS	H9 Cell Line	embryonic stem cell
19	chr1:45985200-45988600	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr1:45985400-45986600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr1:45985400-45986600	Weak transcription	Fetal Heart	heart
22	chr1:45985400-45986600	Active TSS	HepG2	liver
23	chr1:45985400-45986800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:45985400-45987200	Active TSS	Right Atrium	heart
25	chr1:45985400-45987800	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr1:45985400-45987800	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr1:45985400-45987800	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr1:45985400-45987800	Active TSS	Muscle Satellite Cultured Cells	--
29	chr1:45985400-45987800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:45985400-45987800	Active TSS	Brain Angular Gyrus	brain
31	chr1:45985400-45987800	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr1:45985400-45987800	Active TSS	HSMM	muscle
33	chr1:45985400-45987800	Active TSS	NHEK	skin
34	chr1:45985400-45988000	Active TSS	Brain Hippocampus Middle	brain
35	chr1:45985400-45988200	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr1:45985400-45988200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:45985400-45988600	Active TSS	Hela-S3	cervix
38	chr1:45985400-45988800	Active TSS	A549	lung
39	chr1:45985600-45986400	Weak transcription	Spleen	Spleen
40	chr1:45985600-45986800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:45985600-45987000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:45985600-45987800	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr1:45985600-45987800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:45985600-45987800	Active TSS	HMEC	breast
45	chr1:45985600-45988000	Active TSS	H1 Cell Line	embryonic stem cell
46	chr1:45985600-45988000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:45985600-45988000	Active TSS	Lung	lung
48	chr1:45985600-45988000	Active TSS	NHDF-Ad	bronchial
49	chr1:45985600-45988200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:45985600-45988200	Active TSS	Fetal Brain Female	brain

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