Variant report

Variant	rs34569417
Chromosome Location	chr3:47843600-47843601
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr3:47843592-47845017	A549	lung:	n/a	n/a
2	GTF2F1	chr3:47843577-47844248	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:47843542-47845381	U87	brain:	n/a	n/a
4	POLR2A	chr3:47843419-47845734	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr3:47843566-47845333	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr3:47843588-47845545	SK-N-SH	brain:	n/a	n/a
7	HCFC1	chr3:47842851-47845382	Hela-S3	cervix:	n/a	n/a
8	GTF3C2	chr3:47843389-47844149	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr3:47843555-47845539	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr3:47843438-47843640	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:47843558-47845224	HepG2	liver:	n/a	n/a
12	TCF7L2	chr3:47843555-47844865	Hela-S3	cervix:	n/a	n/a
13	RPC155	chr3:47843228-47843924	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr3:47843489-47845342	Hela-S3	cervix:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:47843314..47845660-chr3:47950504..47953455,2	MCF-7	breast:
2	chr3:47841394..47846517-chr3:47861978..47869167,10	MCF-7	breast:
3	chr3:47842553..47846144-chr3:47865369..47869227,6	MCF-7	breast:
4	chr3:47843334..47845793-chr3:48129178..48132338,3	K562	blood:
5	chr3:47420645..47423127-chr3:47843323..47845540,2	K562	blood:
6	chr3:47819738..47825460-chr3:47843094..47847845,6	K562	blood:
7	chr3:47843334..47845793-chr3:48129706..48132338,2	K562	blood:
8	chr3:47821014..47824119-chr3:47842599..47847365,10	K562	blood:
9	chr3:47420645..47423127-chr3:47843323..47847023,3	K562	blood:
10	chr3:47821442..47824826-chr3:47842672..47846080,5	MCF-7	breast:
11	chr3:47694842..47697833-chr3:47842535..47844338,2	MCF-7	breast:

No data

Variant related genes	Relation type
DHX30	TF binding region
ENSG00000047849	Chromatin interaction
ENSG00000076201	Chromatin interaction
ENSG00000260236	Chromatin interaction
ENSG00000173473	Chromatin interaction
ENSG00000132153	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1061003	0.86[AFR][1000 genomes]
rs10865948	0.80[AMR][1000 genomes]
rs11130145	0.87[AMR][1000 genomes]
rs11130146	0.88[AMR][1000 genomes]
rs11130147	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11130148	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11130150	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11708849	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11710199	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11712464	0.86[EUR][1000 genomes]
rs11714942	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11716582	0.81[AMR][1000 genomes]
rs11927129	0.86[EUR][1000 genomes]
rs12492915	0.83[AMR][1000 genomes]
rs12495204	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12497921	0.83[AMR][1000 genomes]
rs12498027	0.85[AMR][1000 genomes]
rs12633604	0.86[AMR][1000 genomes]
rs13061412	0.84[AMR][1000 genomes]
rs13063042	0.85[AMR][1000 genomes]
rs13064183	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13070035	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13077230	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13079407	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13081356	0.87[AMR][1000 genomes]
rs13086149	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13091913	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13094264	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13098128	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1403578	0.81[AMR][1000 genomes]
rs1403579	0.81[AMR][1000 genomes]
rs1486915	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1684942	0.86[AFR][1000 genomes]
rs17079785	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17290490	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2030596	0.83[AMR][1000 genomes]
rs2047559	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2049301	0.82[AMR][1000 genomes]
rs2101398	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2133601	0.85[AMR][1000 genomes]
rs2140335	0.88[AMR][1000 genomes]
rs2293226	0.81[AMR][1000 genomes]
rs2631721	0.84[AFR][1000 genomes]
rs2882611	0.81[AMR][1000 genomes]
rs2882668	0.81[AFR][1000 genomes]
rs319680	0.85[AFR][1000 genomes]
rs319682	0.83[AFR][1000 genomes]
rs319684	0.83[AFR][1000 genomes]
rs319685	0.82[AFR][1000 genomes]
rs319687	0.85[AFR][1000 genomes]
rs319689	0.85[AFR][1000 genomes]
rs319690	0.83[AFR][1000 genomes]
rs319691	0.82[AFR][1000 genomes]
rs319693	0.85[EUR][1000 genomes]
rs319694	0.87[AFR][1000 genomes]
rs34249203	0.83[EUR][1000 genomes]
rs34351471	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34777284	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34906469	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35148469	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35582375	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs35698005	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3755638	0.80[AMR][1000 genomes]
rs3772399	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3772403	0.80[AMR][1000 genomes]
rs3888	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3915654	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4410463	0.82[AMR][1000 genomes]
rs4858801	0.81[AMR][1000 genomes]
rs4858803	0.83[AMR][1000 genomes]
rs4858842	0.81[AMR][1000 genomes]
rs4858846	0.85[AMR][1000 genomes]
rs4858851	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4858853	0.91[EUR][1000 genomes]
rs4858857	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4858860	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4858863	0.95[EUR][1000 genomes]
rs55823596	0.90[EUR][1000 genomes]
rs56376646	0.86[EUR][1000 genomes]
rs61181421	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61620099	0.81[AMR][1000 genomes]
rs62262129	0.84[AMR][1000 genomes]
rs62263561	0.90[EUR][1000 genomes]
rs62263575	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6442074	0.85[AMR][1000 genomes]
rs6442079	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6442081	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6442082	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6442083	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6442085	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6442086	0.93[EUR][1000 genomes]
rs6768699	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6772301	0.85[AMR][1000 genomes]
rs6773467	0.82[AMR][1000 genomes]
rs6773732	0.82[AMR][1000 genomes]
rs6774170	0.80[AMR][1000 genomes]
rs6776963	0.95[EUR][1000 genomes]
rs6777632	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6782998	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6785669	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6786001	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6792350	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6792497	0.84[AMR][1000 genomes]
rs6792737	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6806860	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72906488	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73085151	0.90[EUR][1000 genomes]
rs7429162	0.82[AMR][1000 genomes]
rs7612219	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7613934	0.83[AMR][1000 genomes]
rs7618758	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7619882	0.81[AFR][1000 genomes]
rs7621236	0.83[AMR][1000 genomes]
rs7624474	0.83[AMR][1000 genomes]
rs7629850	0.95[EUR][1000 genomes]
rs7631950	0.81[AMR][1000 genomes]
rs7637372	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7637950	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7638103	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7645846	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7646982	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7649393	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7653368	0.82[AFR][1000 genomes]
rs777015	0.81[AFR][1000 genomes]
rs800762	0.86[AFR][1000 genomes]
rs810334	0.81[AFR][1000 genomes]
rs868255	0.81[AMR][1000 genomes]
rs870622	0.81[AMR][1000 genomes]
rs883661	0.81[AMR][1000 genomes]
rs9757517	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9850154	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003072	chr3:47673628-47869154	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv834679	chr3:47749475-47924006	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
3	nsv965333	chr3:47815622-47845296	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv10270	chr3:47822606-47845578	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs34569417	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs34569417	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs34569417	ZNF589	cis	Nerve Tibial	GTEx
rs34569417	MRPS18AP1	cis	Nerve Tibial	GTEx
rs34569417	DHX30	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:144 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47833600-47843600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:47840800-47843800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:47841800-47843600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:47842600-47843600	Enhancers	Colonic Mucosa	Colon
5	chr3:47842800-47843600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:47842800-47843800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:47843000-47843600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:47843000-47843600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:47843000-47843600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:47843000-47843600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:47843000-47843600	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr3:47843000-47843600	Enhancers	Muscle Satellite Cultured Cells	--
13	chr3:47843000-47843600	Enhancers	A549	lung
14	chr3:47843000-47843600	Enhancers	Dnd41	blood
15	chr3:47843000-47843600	Enhancers	HMEC	breast
16	chr3:47843000-47843600	Enhancers	K562	blood
17	chr3:47843000-47843600	Enhancers	NHEK	skin
18	chr3:47843000-47843600	Enhancers	Osteobl	bone
19	chr3:47843000-47843800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:47843000-47843800	Enhancers	Stomach Mucosa	stomach
21	chr3:47843000-47844400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:47843200-47843600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:47843200-47843600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:47843200-47843600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:47843200-47843600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr3:47843200-47843600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:47843200-47843600	Enhancers	Liver	Liver
28	chr3:47843200-47843600	Enhancers	Brain Hippocampus Middle	brain
29	chr3:47843200-47843600	Enhancers	Colon Smooth Muscle	Colon
30	chr3:47843200-47843600	Weak transcription	Fetal Lung	lung
31	chr3:47843200-47843600	Enhancers	Fetal Muscle Leg	muscle
32	chr3:47843200-47843600	Enhancers	Fetal Thymus	thymus
33	chr3:47843200-47843600	Enhancers	Pancreas	Pancrea
34	chr3:47843200-47843600	Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr3:47843200-47843600	Enhancers	Stomach Smooth Muscle	stomach
36	chr3:47843200-47843600	Enhancers	HSMM	muscle
37	chr3:47843200-47843600	Enhancers	NHLF	lung
38	chr3:47843200-47843800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr3:47843200-47843800	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr3:47843200-47843800	Flanking Active TSS	Fetal Heart	heart
41	chr3:47843200-47843800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:47843200-47843800	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr3:47843200-47845000	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr3:47843200-47845200	Active TSS	Duodenum Mucosa	Duodenum
45	chr3:47843200-47845800	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr3:47843400-47843600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:47843400-47843600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:47843400-47843600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:47843400-47843600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:47843400-47843600	Weak transcription	Brain Anterior Caudate	brain

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