Variant report

Variant	rs4858881
Chromosome Location	chr3:48123796-48123797
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48121824..48127191-chr3:48127518..48131835,8	K562	blood:
2	chr3:48122929..48125940-chr3:48127002..48131187,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000047849	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1013431	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10446426	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1060407	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs11130152	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11130154	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11130155	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1137524	0.82[EUR][1000 genomes]
rs11707679	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs11710866	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11711129	0.86[EUR][1000 genomes]
rs11714518	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11720151	0.91[CEU][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11924107	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12486714	0.92[CEU][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12493348	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13074973	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13075457	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13075795	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13080997	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13081463	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13085054	0.91[CEU][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs13089844	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13093830	0.82[EUR][1000 genomes]
rs1530646	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1550914	0.92[EUR][1000 genomes]
rs184388	0.82[EUR][1000 genomes]
rs2034963	0.81[EUR][1000 genomes]
rs2053767	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2121754	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2166770	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2166772	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2361683	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2361684	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28637561	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2882668	0.82[EUR][1000 genomes]
rs319684	0.82[EUR][1000 genomes]
rs319685	0.82[EUR][1000 genomes]
rs319686	0.82[EUR][1000 genomes]
rs319689	0.81[EUR][1000 genomes]
rs319690	0.80[EUR][1000 genomes]
rs319696	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs34025851	0.82[EUR][1000 genomes]
rs34597784	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34750113	0.83[EUR][1000 genomes]
rs35199727	0.82[EUR][1000 genomes]
rs35314534	0.92[EUR][1000 genomes]
rs35689209	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732529	0.82[EUR][1000 genomes]
rs4293721	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4296617	0.92[EUR][1000 genomes]
rs4392441	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4599334	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs4858810	0.92[CEU][hapmap]
rs4858871	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs4858876	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4858880	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4858882	0.87[EUR][1000 genomes]
rs4858887	0.93[EUR][1000 genomes]
rs5012971	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56067795	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60446735	0.82[EUR][1000 genomes]
rs62260830	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6442090	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6442091	0.92[EUR][1000 genomes]
rs6442094	0.88[EUR][1000 genomes]
rs6442096	0.89[EUR][1000 genomes]
rs6442099	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6442101	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs6442102	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6766641	0.87[EUR][1000 genomes]
rs6768318	0.87[EUR][1000 genomes]
rs6770467	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6770477	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6771917	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6772396	0.82[EUR][1000 genomes]
rs6773208	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6777081	0.84[EUR][1000 genomes]
rs6783629	0.81[EUR][1000 genomes]
rs6791834	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793477	0.83[AMR][1000 genomes]
rs6803741	0.95[CEU][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6804520	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6806820	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7374482	0.92[CEU][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7374516	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7426976	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7427418	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7427648	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7430879	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7430913	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7618163	0.84[EUR][1000 genomes]
rs7619882	0.83[EUR][1000 genomes]
rs7620736	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7627645	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7642590	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs7649981	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7651237	0.83[EUR][1000 genomes]
rs7653368	0.82[EUR][1000 genomes]
rs777015	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs777017	0.82[EUR][1000 genomes]
rs796566	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs810334	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs936428	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9811277	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9812875	0.83[EUR][1000 genomes]
rs9814961	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9825114	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs9828959	0.84[EUR][1000 genomes]
rs9842649	0.82[EUR][1000 genomes]
rs9846062	0.92[EUR][1000 genomes]
rs9854454	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9860485	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9862913	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1001056	chr3:47912342-48223849	Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv1012828	chr3:47996472-48192862	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv876760	chr3:48019258-48197614	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv834681	chr3:48032000-48181775	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1004557	chr3:48056534-48256694	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers 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 miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv1012024	chr3:48119229-48242670	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4858881	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs4858881	MRPS18AP1	cis	Thyroid	GTEx
rs4858881	ZNF589	cis	Nerve Tibial	GTEx
rs4858881	MRPS18AP1	cis	Nerve Tibial	GTEx
rs4858881	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs4858881	CDC25A	cis	Thyroid	GTEx
rs4858881	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs4858881	NME6	cis	Esophagus Muscularis	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48051200-48128000	Weak transcription	Primary B cells from cord blood	blood
2	chr3:48059600-48128800	Weak transcription	Primary T cells from cord blood	blood
3	chr3:48064400-48128800	Weak transcription	Esophagus	oesophagus
4	chr3:48081400-48128400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:48081800-48128400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:48089400-48128400	Weak transcription	Thymus	Thymus
7	chr3:48089400-48128600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:48089600-48128400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:48089800-48128200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:48089800-48128800	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr3:48093800-48128400	Weak transcription	Spleen	Spleen
12	chr3:48095000-48128400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr3:48096600-48126000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:48100800-48128400	Weak transcription	Brain Substantia Nigra	brain
15	chr3:48100800-48128600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr3:48100800-48128800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:48101600-48128200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:48103600-48128200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:48105000-48128200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:48105200-48125600	Weak transcription	Dnd41	blood
21	chr3:48105200-48128400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr3:48105600-48128200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:48106000-48126000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:48106000-48128400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:48106600-48128400	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:48106600-48128800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:48107400-48125800	Weak transcription	Pancreas	Pancrea
28	chr3:48108400-48128800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:48108800-48128200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:48109000-48127600	Weak transcription	Brain Germinal Matrix	brain
31	chr3:48109000-48128400	Weak transcription	Fetal Brain Male	brain
32	chr3:48110200-48128200	Weak transcription	Fetal Brain Female	brain
33	chr3:48110200-48128400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr3:48110800-48124000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr3:48111000-48123800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr3:48111000-48128400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:48111200-48123800	Weak transcription	Liver	Liver
38	chr3:48111200-48125200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:48111400-48126800	Weak transcription	NH-A	brain
40	chr3:48112800-48126400	Weak transcription	Fetal Lung	lung
41	chr3:48113000-48125200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:48113200-48123800	Weak transcription	HepG2	liver
43	chr3:48113200-48124000	Weak transcription	Fetal Intestine Large	intestine
44	chr3:48113200-48128200	Weak transcription	HSMMtube	muscle
45	chr3:48113200-48128400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr3:48113400-48125600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:48113400-48128800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:48113600-48128800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:48113800-48127800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:48114400-48126000	Weak transcription	Stomach Smooth Muscle	stomach

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