Variant report

Variant	rs4858857
Chromosome Location	chr3:47813212-47813213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47809506..47818715-chr3:47820075..47824996,15	MCF-7	breast:
2	chr3:47808223..47811235-chr3:47813033..47816575,4	MCF-7	breast:
3	chr3:47812305..47815018-chr3:47821120..47824532,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173473	Chromatin interaction
ENSG00000266457	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10865948	0.85[AMR][1000 genomes]
rs11130138	0.81[AMR][1000 genomes]
rs11130143	0.86[AMR][1000 genomes]
rs11130144	0.86[AMR][1000 genomes]
rs11130145	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11130146	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11130147	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130148	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130150	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11708849	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11710199	0.85[EUR][1000 genomes]
rs11712464	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11714942	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11716582	0.86[AMR][1000 genomes]
rs11927129	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12492915	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12495204	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12497921	0.91[AMR][1000 genomes]
rs12498027	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12633604	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12635438	0.84[EUR][1000 genomes]
rs12636863	0.86[AMR][1000 genomes]
rs13061412	0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13063042	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13064183	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13070035	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13077230	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13079407	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13081356	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13086149	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13091913	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13094264	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13098128	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13319205	0.82[EUR][1000 genomes]
rs1403578	0.89[AMR][1000 genomes]
rs1403579	0.89[AMR][1000 genomes]
rs1464614	0.86[AMR][1000 genomes]
rs1486915	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17079785	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17290490	0.85[EUR][1000 genomes]
rs2030596	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2047559	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2049301	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2101398	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2133601	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2140335	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2293226	0.86[AMR][1000 genomes]
rs2351248	0.86[ASN][1000 genomes]
rs2882611	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs319693	0.85[EUR][1000 genomes]
rs34351471	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34569417	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34777284	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34906469	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35148469	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35582375	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35664069	0.82[EUR][1000 genomes]
rs35698005	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3755637	0.84[AMR][1000 genomes]
rs3755638	0.85[AMR][1000 genomes]
rs3772399	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3772403	0.85[AMR][1000 genomes]
rs3888	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3915654	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4274776	0.84[AMR][1000 genomes]
rs4410463	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4858801	0.86[AMR][1000 genomes]
rs4858803	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4858836	0.81[AMR][1000 genomes]
rs4858842	0.89[AMR][1000 genomes]
rs4858846	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4858851	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4858853	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4858860	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4858863	0.94[EUR][1000 genomes]
rs55823596	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56376646	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56746603	0.83[AMR][1000 genomes]
rs60110914	0.84[AMR][1000 genomes]
rs61181421	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61620099	0.86[AMR][1000 genomes]
rs62262129	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62263561	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62263575	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6442072	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6442074	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6442079	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6442081	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6442082	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442083	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442085	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6442086	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6768699	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6772301	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6773467	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6773732	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6774170	0.87[AMR][1000 genomes]
rs6776963	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6777632	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6782998	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6785031	0.81[AMR][1000 genomes]
rs6785669	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6786001	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6792350	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6792497	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6792737	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6806860	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72906474	0.85[ASN][1000 genomes]
rs72906488	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73085151	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7429162	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7612219	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7613934	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7618758	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7621236	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7624474	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7629850	0.94[EUR][1000 genomes]
rs7631950	0.86[AMR][1000 genomes]
rs7637372	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7637950	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7638103	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7645846	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7646982	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7649393	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs868255	0.89[AMR][1000 genomes]
rs870622	0.89[AMR][1000 genomes]
rs883661	0.89[AMR][1000 genomes]
rs883663	0.87[AMR][1000 genomes]
rs9757517	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9850154	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv876758	chr3:47681881-47842234	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
3	nsv876759	chr3:47725315-47830741	Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
4	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
5	nsv590233	chr3:47798700-47829277	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4858857	ZNF589	cis	Nerve Tibial	GTEx
rs4858857	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs4858857	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs4858857	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs4858857	MRPS18AP1	cis	Nerve Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47701600-47819800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:47727600-47819400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:47769800-47817800	Weak transcription	Pancreas	Pancrea
4	chr3:47772800-47821000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:47774200-47820600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:47777000-47817600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:47777200-47813600	Weak transcription	A549	lung
8	chr3:47777200-47819000	Weak transcription	Fetal Brain Male	brain
9	chr3:47777200-47819800	Weak transcription	Small Intestine	intestine
10	chr3:47777400-47819800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:47777400-47821000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:47777400-47821000	Weak transcription	Brain Substantia Nigra	brain
13	chr3:47777400-47821800	Weak transcription	Right Ventricle	heart
14	chr3:47777600-47820600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:47777600-47820800	Weak transcription	NHLF	lung
16	chr3:47778800-47814200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:47784000-47816000	Strong transcription	Fetal Stomach	stomach
18	chr3:47784800-47820800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:47786600-47814200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:47787400-47820800	Weak transcription	Brain Angular Gyrus	brain
21	chr3:47788000-47813600	Weak transcription	HUVEC	blood vessel
22	chr3:47793000-47818000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:47793800-47814800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:47794800-47819400	Weak transcription	Right Atrium	heart
25	chr3:47795800-47814600	Strong transcription	Fetal Thymus	thymus
26	chr3:47797800-47814600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:47798000-47815000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:47798000-47816600	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:47798800-47821000	Weak transcription	Brain Anterior Caudate	brain
30	chr3:47800000-47820800	Weak transcription	HSMMtube	muscle
31	chr3:47800600-47814600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr3:47801200-47814800	Strong transcription	Dnd41	blood
33	chr3:47801400-47814800	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:47801800-47814800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:47802000-47813600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:47802800-47814600	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr3:47802800-47822000	Weak transcription	Aorta	Aorta
38	chr3:47804000-47816000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr3:47804000-47816400	Weak transcription	Ovary	ovary
40	chr3:47804200-47813400	Weak transcription	Fetal Heart	heart
41	chr3:47804200-47815200	Strong transcription	Fetal Intestine Small	intestine
42	chr3:47804200-47819000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:47805200-47815200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:47805200-47819000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:47805600-47814200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:47805600-47820800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr3:47806200-47813400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:47806200-47820800	Weak transcription	Colonic Mucosa	Colon
49	chr3:47806200-47821600	Weak transcription	Esophagus	oesophagus
50	chr3:47806400-47813600	Weak transcription	NH-A	brain

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