Variant report

Variant	rs2883059
Chromosome Location	chr3:49902160-49902161
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr3:49901968-49902504	HepG2	liver:	n/a	chr3:49902130-49902150 chr3:49902132-49902148 chr3:49902133-49902147
2	MAFK	chr3:49901991-49902259	IMR90	lung:	n/a	chr3:49902130-49902150 chr3:49902132-49902148 chr3:49902133-49902147
3	MAFK	chr3:49901980-49902313	K562	blood:	n/a	chr3:49902130-49902150 chr3:49902132-49902148 chr3:49902133-49902147
4	MAFK	chr3:49901979-49902277	H1-hESC	embryonic stem cell:	n/a	chr3:49902130-49902150 chr3:49902132-49902148 chr3:49902133-49902147
5	MAFK	chr3:49902037-49902311	Hela-S3	cervix:	n/a	chr3:49902130-49902150 chr3:49902132-49902148 chr3:49902133-49902147
6	MAFF	chr3:49901982-49902291	HepG2	liver:	n/a	chr3:49902133-49902147 chr3:49902127-49902145
7	MAFK	chr3:49901960-49902565	HepG2	liver:	n/a	chr3:49902512-49902526 chr3:49902514-49902525 chr3:49902130-49902150 chr3:49902509-49902525 chr3:49902514-49902525 chr3:49902132-49902148 chr3:49902133-49902147
8	MAFF	chr3:49902065-49902283	K562	blood:	n/a	chr3:49902133-49902147 chr3:49902127-49902145

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49897257..49899653-chr3:49900081..49902662,3	K562	blood:

Variant related genes	Relation type
CAMKV	TF binding region
RN7SL217P	TF binding region
ENSG00000164076	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1062633	0.81[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs11130222	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130228	0.81[JPT][hapmap]
rs11130233	0.89[JPT][hapmap]
rs11709573	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11712056	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11714324	0.92[ASN][1000 genomes]
rs11721204	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12496973	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs12634780	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs13060128	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs13077403	0.87[ASN][1000 genomes]
rs13079006	0.84[ASN][1000 genomes]
rs13082703	0.84[ASN][1000 genomes]
rs17657664	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[ASN][1000 genomes]
rs17657688	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[ASN][1000 genomes]
rs2230590	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs2252833	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs2280406	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs2352969	0.89[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2352984	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2353579	0.82[JPT][hapmap]
rs2526747	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs2526748	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs2526751	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs2624819	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2624821	0.89[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2624832	0.84[ASN][1000 genomes]
rs2624843	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs2681776	0.84[ASN][1000 genomes]
rs2681779	0.89[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2681780	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs2681781	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs2777888	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs2883057	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs34034116	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34312088	0.84[ASN][1000 genomes]
rs34654589	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35275715	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36022378	0.94[ASN][1000 genomes]
rs3733134	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3774733	0.82[JPT][hapmap]
rs3774759	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3796386	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688688	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4688689	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs4688690	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs4688753	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4688755	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs4688758	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs55692411	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62262114	0.84[ASN][1000 genomes]
rs6446193	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs6762477	0.87[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs6765484	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs6771546	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs6772095	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs6774354	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6792892	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs6793528	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7430334	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs7613360	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7613875	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs7615206	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7621026	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs7621352	0.82[JPT][hapmap]
rs7626952	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7627864	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7627910	0.87[ASN][1000 genomes]
rs7628058	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs7648174	0.84[ASN][1000 genomes]
rs868891	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9311446	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs952594	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9814664	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs9821675	0.90[JPT][hapmap]
rs9861216	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs9866695	0.88[CHD][hapmap];0.82[JPT][hapmap]

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	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer 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	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs2883059	QRICH1	cis	cerebellum	SCAN
rs2883059	RBM6	cis	parietal	SCAN
rs2883059	RBM6	cis	Artery Aorta	GTEx
rs2883059	RNF123	cis	cerebellum	SCAN
rs2883059	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs2883059	HYAL3	cis	multi-tissue	Pritchard
rs2883059	RBM6	cis	Artery Tibial	GTEx
rs2883059	RBM6	cis	Nerve Tibial	GTEx
rs2883059	RBM6	cis	multi-tissue	Pritchard
rs2883059	RBM6	cis	Esophagus Muscularis	GTEx
rs2883059	RBM6	cis	lymphoblastoid	seeQTL
rs2883059	ARIH2	cis	cerebellum	SCAN
rs2883059	RBM6	cis	Whole Blood	GTEx
rs2883059	RBM6	cis	Thyroid	GTEx
rs2883059	RNF123	cis	parietal	SCAN
rs2883059	RBM6	cis	Heart Left Ventricle	GTEx
rs2883059	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs2883059	RBM6	cis	Stomach	GTEx
rs2883059	CELSR3	cis	parietal	SCAN
rs2883059	RBM6	cis	cerebellum	SCAN
rs2883059	RBM6	cis	Esophagus Mucosa	GTEx
rs2883059	RBM6	cis	lung	GTEx
rs2883059	RBM6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49894600-49903000	Weak transcription	Gastric	stomach
2	chr3:49894600-49903600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:49894600-49903800	Weak transcription	Fetal Intestine Large	intestine
4	chr3:49894600-49904200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:49894600-49906400	Weak transcription	Right Atrium	heart
6	chr3:49897000-49902800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:49898400-49902400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:49898400-49905000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:49899000-49904200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:49899000-49904800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:49899400-49902400	Weak transcription	Brain Anterior Caudate	brain
12	chr3:49899400-49902600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:49899400-49903400	Weak transcription	Brain Germinal Matrix	brain
14	chr3:49899800-49904800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:49899800-49905400	Weak transcription	Fetal Intestine Small	intestine
16	chr3:49901000-49905200	Enhancers	Fetal Brain Male	brain
17	chr3:49901600-49902600	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr3:49901600-49906000	Enhancers	H1 Cell Line	embryonic stem cell
19	chr3:49901600-49906400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:49901800-49902600	Active TSS	Fetal Brain Female	brain
21	chr3:49901800-49903400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:49901800-49904000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
23	chr3:49902000-49902200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:49902000-49902400	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
25	chr3:49902000-49902600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
26	chr3:49902000-49903200	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr3:49902000-49903200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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