Variant report

Variant	rs34673142
Chromosome Location	chr1:45985561-45985562
allele	C/T
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:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:45984510..45988941-chr1:46031540..46035902,8	MCF-7	breast:
2	chr1:45973182..45975128-chr1:45984664..45989019,3	MCF-7	breast:
3	chr1:45985173..45987673-chr1:46047489..46052049,5	MCF-7	breast:
4	chr1:45982342..45989534-chr1:46006947..46020678,57	K562	blood:
5	chr1:45975860..45989626-chr1:46030076..46041078,36	K562	blood:
6	chr1:45283995..45285689-chr1:45985443..45988306,2	K562	blood:
7	chr1:45976870..45989534-chr1:46007918..46019226,54	K562	blood:
8	chr1:45984465..45989261-chr1:46150683..46156386,7	K562	blood:
9	chr1:45805652..45808329-chr1:45985496..45987569,2	K562	blood:
10	chr1:45982844..45990993-chr1:46030121..46038313,25	K562	blood:
11	chr1:45980210..45995142-chr1:46046095..46057139,89	K562	blood:
12	chr1:45974558..45995867-chr1:46046173..46057010,94	K562	blood:
13	chr1:43291298..43293447-chr1:45985281..45987482,2	K562	blood:
14	chr1:45770153..45772059-chr1:45985117..45987576,2	K562	blood:
15	chr1:45984460..45986056-chr1:46058706..46061606,2	K562	blood:
16	chr1:45985342..45989391-chr1:46011113..46019467,18	MCF-7	breast:
17	chr1:45982735..45988890-chr1:46031987..46038228,10	MCF-7	breast:
18	chr1:45969960..45972308-chr1:45985412..45987180,2	MCF-7	breast:
19	chr1:45984572..45987422-chr1:46019368..46021467,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000117448	Chromatin interaction
ENSG00000159596	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000162415	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1006216	0.81[EUR][1000 genomes]
rs10789464	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10890330	0.87[EUR][1000 genomes]
rs11211111	0.80[EUR][1000 genomes]
rs11211117	0.81[EUR][1000 genomes]
rs11211118	0.81[EUR][1000 genomes]
rs11211123	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211124	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11211128	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11211137	0.82[EUR][1000 genomes]
rs11211139	0.83[EUR][1000 genomes]
rs12029322	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12037201	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12042903	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12049503	0.82[EUR][1000 genomes]
rs12066142	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12067642	0.87[EUR][1000 genomes]
rs12077621	0.83[EUR][1000 genomes]
rs12564806	0.85[EUR][1000 genomes]
rs2055145	0.87[EUR][1000 genomes]
rs28555082	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2883968	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34768551	0.83[EUR][1000 genomes]
rs3790583	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4633317	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660858	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4660863	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5015340	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55642258	0.87[EUR][1000 genomes]
rs61788281	0.81[EUR][1000 genomes]
rs61788285	0.87[EUR][1000 genomes]
rs61788336	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788356	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67683090	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs713358	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7528573	0.81[EUR][1000 genomes]
rs868351	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9727262	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9729395	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs34673142	C2orf49	trans	lymphoblastoid	RTeQTL
rs34673142	TESK2	cis	Whole Blood	GTEx
rs34673142	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs34673142	MMACHC	cis	multi-tissue	Pritchard
rs34673142	PRDX1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45981000-45986000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:45983200-45986000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:45983200-45986000	Weak transcription	Gastric	stomach
4	chr1:45983200-45986400	Weak transcription	Pancreas	Pancrea
5	chr1:45983600-45986000	Enhancers	Fetal Brain Male	brain
6	chr1:45983800-45986000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:45984400-45985600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
8	chr1:45984400-45985600	Flanking Active TSS	GM12878-XiMat	blood
9	chr1:45984400-45985800	Enhancers	Stomach Mucosa	stomach
10	chr1:45984400-45986000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:45984400-45986000	Enhancers	Primary B cells from cord blood	blood
12	chr1:45984400-45986000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:45984400-45986000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr1:45984400-45986000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:45984400-45986000	Enhancers	Fetal Lung	lung
16	chr1:45984400-45986000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr1:45984400-45986400	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr1:45984600-45985600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:45984600-45985600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:45984600-45985600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr1:45984600-45985600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:45984600-45985600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:45984600-45985800	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr1:45984600-45986000	Enhancers	Primary B cells from peripheral blood	blood
25	chr1:45984600-45986000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr1:45984600-45986000	Enhancers	Fetal Muscle Leg	muscle
27	chr1:45984600-45986200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr1:45984600-45986200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:45984600-45987000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:45984800-45985600	Genic enhancers	Fetal Intestine Small	intestine
31	chr1:45984800-45985600	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr1:45984800-45985800	Enhancers	Ovary	ovary
33	chr1:45984800-45986000	Enhancers	Thymus	Thymus
34	chr1:45984800-45986200	Flanking Active TSS	HUVEC	blood vessel
35	chr1:45985000-45985600	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
36	chr1:45985000-45985600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:45985000-45985600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:45985000-45985600	Genic enhancers	Fetal Stomach	stomach
39	chr1:45985000-45985600	Enhancers	Spleen	Spleen
40	chr1:45985000-45985600	Flanking Active TSS	NHDF-Ad	bronchial
41	chr1:45985000-45985800	Enhancers	Aorta	Aorta
42	chr1:45985000-45985800	Enhancers	Colonic Mucosa	Colon
43	chr1:45985000-45985800	Enhancers	Placenta	Placenta
44	chr1:45985000-45986000	Enhancers	Primary T cells fromperipheralblood	blood
45	chr1:45985000-45986000	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr1:45985000-45986000	Enhancers	Fetal Thymus	thymus
47	chr1:45985000-45986000	Enhancers	Left Ventricle	heart
48	chr1:45985000-45986000	Enhancers	Psoas Muscle	Psoas
49	chr1:45985000-45986200	Flanking Active TSS	Liver	Liver
50	chr1:45985000-45986200	Enhancers	Sigmoid Colon	Sigmoid Colon

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