Variant report

Variant	rs34005367
Chromosome Location	chr3:52558904-52558905
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52554843..52559532-chr3:52566910..52570402,7	MCF-7	breast:
2	chr3:52551111..52554473-chr3:52556873..52560591,3	MCF-7	breast:
3	chr3:52553170..52556656-chr3:52557821..52561228,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010327	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000168273	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10510760	0.82[ASN][1000 genomes]
rs11130307	0.83[ASN][1000 genomes]
rs11130308	0.81[ASN][1000 genomes]
rs1133415	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11708075	0.83[ASN][1000 genomes]
rs11709284	0.93[ASN][1000 genomes]
rs11709448	0.82[ASN][1000 genomes]
rs11711421	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11714419	0.84[ASN][1000 genomes]
rs11714565	0.83[ASN][1000 genomes]
rs11717043	0.81[ASN][1000 genomes]
rs11718420	0.81[ASN][1000 genomes]
rs11718509	0.81[ASN][1000 genomes]
rs11720159	0.80[ASN][1000 genomes]
rs11720432	0.81[ASN][1000 genomes]
rs12486847	0.81[ASN][1000 genomes]
rs12487445	0.80[ASN][1000 genomes]
rs12487591	0.81[ASN][1000 genomes]
rs12489732	0.99[ASN][1000 genomes]
rs12489828	0.93[ASN][1000 genomes]
rs12498066	0.81[ASN][1000 genomes]
rs12629701	0.81[ASN][1000 genomes]
rs12632381	0.83[ASN][1000 genomes]
rs13059862	0.94[ASN][1000 genomes]
rs13060048	0.94[ASN][1000 genomes]
rs13063160	0.94[ASN][1000 genomes]
rs13064064	0.81[ASN][1000 genomes]
rs13065851	0.82[ASN][1000 genomes]
rs13068293	0.80[ASN][1000 genomes]
rs13076398	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13081028	0.82[ASN][1000 genomes]
rs13085331	0.81[ASN][1000 genomes]
rs13303	0.92[ASN][1000 genomes]
rs13621	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1561337	0.81[ASN][1000 genomes]
rs1570	0.96[ASN][1000 genomes]
rs17052256	0.96[ASN][1000 genomes]
rs17052259	0.96[ASN][1000 genomes]
rs17264436	0.84[ASN][1000 genomes]
rs1821879	0.92[ASN][1000 genomes]
rs1961958	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1961959	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2015971	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2118540	0.83[ASN][1000 genomes]
rs2164884	0.81[ASN][1000 genomes]
rs2251219	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2289249	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2336145	0.83[ASN][1000 genomes]
rs2336146	0.81[ASN][1000 genomes]
rs28661185	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2878628	0.96[ASN][1000 genomes]
rs33964154	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34115864	0.83[ASN][1000 genomes]
rs34173654	0.82[ASN][1000 genomes]
rs34215106	0.81[ASN][1000 genomes]
rs34537256	0.81[ASN][1000 genomes]
rs34754793	0.81[ASN][1000 genomes]
rs34954168	0.83[ASN][1000 genomes]
rs35107891	0.84[ASN][1000 genomes]
rs35249778	0.81[ASN][1000 genomes]
rs35409678	0.80[ASN][1000 genomes]
rs3733045	0.81[ASN][1000 genomes]
rs3755806	0.81[ASN][1000 genomes]
rs3774365	0.81[ASN][1000 genomes]
rs3774366	0.81[ASN][1000 genomes]
rs3796353	0.96[ASN][1000 genomes]
rs3852066	0.81[ASN][1000 genomes]
rs4234633	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4282054	0.93[ASN][1000 genomes]
rs4434138	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4475032	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687546	0.83[ASN][1000 genomes]
rs4687547	0.83[ASN][1000 genomes]
rs4687624	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687625	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687626	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687629	0.81[ASN][1000 genomes]
rs4687633	0.81[ASN][1000 genomes]
rs4687636	0.81[ASN][1000 genomes]
rs4687637	0.81[ASN][1000 genomes]
rs4687638	0.82[ASN][1000 genomes]
rs4687639	0.81[ASN][1000 genomes]
rs62253700	0.83[ASN][1000 genomes]
rs62253703	0.81[ASN][1000 genomes]
rs62253733	0.82[ASN][1000 genomes]
rs62256903	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6445528	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66782572	0.82[ASN][1000 genomes]
rs6762457	0.83[ASN][1000 genomes]
rs6778735	0.93[ASN][1000 genomes]
rs6778844	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6786043	0.91[ASN][1000 genomes]
rs6786919	0.94[ASN][1000 genomes]
rs6788887	0.94[ASN][1000 genomes]
rs6788993	0.94[ASN][1000 genomes]
rs6790330	0.80[ASN][1000 genomes]
rs6798246	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68021750	0.83[ASN][1000 genomes]
rs6805156	0.83[ASN][1000 genomes]
rs7614498	0.80[ASN][1000 genomes]
rs7614981	0.93[ASN][1000 genomes]
rs7623199	0.83[ASN][1000 genomes]
rs7625743	0.83[ASN][1000 genomes]
rs7628578	0.81[ASN][1000 genomes]
rs7636227	0.94[ASN][1000 genomes]
rs7638808	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7652191	0.83[ASN][1000 genomes]
rs9758945	0.90[ASN][1000 genomes]
rs9917834	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	63 gene(s)	inside rSNPs	diseases
7	nsv590305	chr3:52535586-52569480	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv590307	chr3:52540773-52572056	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv876795	chr3:52544470-52572056	Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
10	nsv876796	chr3:52549676-52572056	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs34005367	GLT8D1	Cis_1M	lymphoblastoid	RTeQTL
rs34005367	ITIH4-AS1	cis	Whole Blood	GTEx
rs34005367	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs34005367	NT5DC2	cis	multi-tissue	Pritchard
rs34005367	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs34005367	MUSTN1	cis	Artery Aorta	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52533400-52559800	Weak transcription	Liver	Liver
2	chr3:52533600-52566000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr3:52535400-52562200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr3:52535600-52562600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr3:52536600-52564000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:52537600-52559800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:52550600-52566600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:52552000-52560800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:52552400-52559200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:52552800-52560600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:52552800-52561200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:52552800-52562000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:52552800-52565400	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:52552800-52566000	Weak transcription	Stomach Mucosa	stomach
15	chr3:52552800-52566200	Weak transcription	Brain Angular Gyrus	brain
16	chr3:52553200-52559400	Weak transcription	Brain Anterior Caudate	brain
17	chr3:52553800-52562000	Weak transcription	K562	blood
18	chr3:52554200-52566000	Weak transcription	HSMM	muscle
19	chr3:52554800-52567200	Weak transcription	Aorta	Aorta
20	chr3:52555400-52565200	Strong transcription	Fetal Intestine Small	intestine
21	chr3:52555600-52559400	Weak transcription	HSMMtube	muscle
22	chr3:52555800-52565200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:52556000-52563600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:52556000-52566000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr3:52556200-52559800	Genic enhancers	Spleen	Spleen
26	chr3:52556200-52563800	Strong transcription	Fetal Brain Female	brain
27	chr3:52556200-52564000	Strong transcription	Brain Germinal Matrix	brain
28	chr3:52556200-52565200	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:52556400-52560800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:52556400-52563600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
31	chr3:52556600-52564200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:52556800-52564200	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr3:52556800-52566400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr3:52557000-52563800	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:52557000-52565800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:52557200-52561000	Weak transcription	GM12878-XiMat	blood
37	chr3:52557200-52563400	Genic enhancers	Right Ventricle	heart
38	chr3:52557200-52563800	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:52557400-52559000	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:52557400-52559600	Genic enhancers	Esophagus	oesophagus
41	chr3:52557400-52559600	Strong transcription	Ovary	ovary
42	chr3:52557400-52559600	Strong transcription	Thymus	Thymus
43	chr3:52557400-52561400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:52557400-52563200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:52557400-52563400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:52557400-52563400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:52557400-52564600	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr3:52557400-52564600	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr3:52557400-52565000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:52557400-52565800	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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