Variant report

Variant	rs55692411
Chromosome Location	chr3:49911155-49911156
allele	A/G
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	HNF4A	chr3:49910989-49911353	HepG2	liver:	n/a	chr3:49911160-49911175
2	HNF4A	chr3:49910974-49911407	HepG2	liver:	n/a	chr3:49911160-49911175
3	SMC3	chr3:49911089-49911371	HepG2	liver:	n/a	n/a
4	HEY1	chr3:49911015-49911350	HepG2	liver:	n/a	n/a
5	RCOR1	chr3:49911030-49911327	HepG2	liver:	n/a	n/a
6	GATA2	chr3:49910886-49911439	SH-SY5Y	brain:	n/a	n/a
7	MAX	chr3:49910990-49911307	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:49910856-49911670	Hela-S3	cervix:	n/a	n/a
9	EP300	chr3:49911064-49911264	HepG2	liver:	n/a	n/a
10	CTCF	chr3:49911140-49911290	Caco-2	colon:	n/a	n/a
11	HNF4G	chr3:49910947-49911335	HepG2	liver:	n/a	chr3:49911159-49911174
12	RAD21	chr3:49911098-49911319	HepG2	liver:	n/a	n/a
13	GATA1	chr3:49910967-49911323	PBDEFetal	blood:	n/a	n/a
14	HDAC2	chr3:49910989-49911318	HepG2	liver:	n/a	n/a
15	YY1	chr3:49910819-49911421	HepG2	liver:	n/a	n/a
16	HNF4A	chr3:49910994-49911367	HepG2	liver:	n/a	chr3:49911160-49911175
17	SP1	chr3:49910943-49911403	HepG2	liver:	n/a	n/a
18	MYC	chr3:49911112-49911206	HepG2	liver:	n/a	n/a
19	GATA3	chr3:49910979-49911333	SH-SY5Y	brain:	n/a	n/a
20	RFX5	chr3:49911145-49911173	HepG2	liver:	n/a	n/a
21	ARID3A	chr3:49911155-49911326	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49900314..49905841-chr3:49909576..49913570,6	K562	blood:
2	chr3:49910943..49912863-chr3:49914615..49917356,2	K562	blood:
3	chr3:49909687..49911283-chr3:49915526..49917285,2	K562	blood:
4	chr3:49906989..49909987-chr3:49910807..49914298,3	K562	blood:

Variant related genes	Relation type
CAMKV	TF binding region
ENSG00000264706	Chromatin interaction
ENSG00000234667	Chromatin interaction
ENSG00000164076	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11130222	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11706185	0.82[AMR][1000 genomes]
rs11709573	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11712056	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11714324	0.90[ASN][1000 genomes]
rs11721204	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13077403	0.88[ASN][1000 genomes]
rs13079006	0.85[ASN][1000 genomes]
rs13082703	0.85[ASN][1000 genomes]
rs17657664	0.85[ASN][1000 genomes]
rs17657688	0.85[ASN][1000 genomes]
rs2352969	0.87[ASN][1000 genomes]
rs2352984	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2624819	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2624821	0.83[ASN][1000 genomes]
rs2624832	0.85[ASN][1000 genomes]
rs2681776	0.85[ASN][1000 genomes]
rs2883059	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34034116	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34312088	0.85[ASN][1000 genomes]
rs34654589	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35275715	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36022378	0.92[ASN][1000 genomes]
rs3733134	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3774759	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3796386	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688688	0.80[ASN][1000 genomes]
rs62262114	0.85[ASN][1000 genomes]
rs6774354	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7613360	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7615206	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7626952	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7627864	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7627910	0.88[ASN][1000 genomes]
rs7648174	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs868891	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs952594	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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	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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs55692411	RBM6	cis	Esophagus Mucosa	GTEx
rs55692411	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs55692411	RBM6	cis	Whole Blood	GTEx
rs55692411	RBM6	cis	Thyroid	GTEx
rs55692411	RBM6	cis	Artery Tibial	GTEx
rs55692411	RBM6	cis	Artery Aorta	GTEx
rs55692411	RBM6	cis	Adipose Subcutaneous	GTEx
rs55692411	RBM6	cis	lung	GTEx
rs55692411	RBM6	cis	Esophagus Muscularis	GTEx
rs55692411	RBM6	cis	Heart Left Ventricle	GTEx
rs55692411	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs55692411	RBM6	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49907800-49911200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:49908000-49911200	Enhancers	Fetal Brain Female	brain
3	chr3:49908000-49913600	Enhancers	Fetal Intestine Large	intestine
4	chr3:49908200-49911600	Enhancers	Brain Anterior Caudate	brain
5	chr3:49908600-49911200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:49908600-49911400	Enhancers	Fetal Intestine Small	intestine
7	chr3:49909800-49911400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:49910000-49911200	Enhancers	Brain Germinal Matrix	brain
9	chr3:49910000-49912400	Enhancers	Stomach Mucosa	stomach
10	chr3:49910000-49917200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:49910200-49911600	Enhancers	Small Intestine	intestine
12	chr3:49910200-49911800	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr3:49910200-49912000	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr3:49910400-49911600	Enhancers	Duodenum Mucosa	Duodenum
15	chr3:49910400-49911800	Enhancers	Colonic Mucosa	Colon
16	chr3:49910400-49911800	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr3:49910600-49911400	Flanking Active TSS	HepG2	liver
18	chr3:49910600-49914800	Weak transcription	Fetal Lung	lung
19	chr3:49910600-49916200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:49910800-49911400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:49910800-49911400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:49910800-49911600	Enhancers	Gastric	stomach
23	chr3:49910800-49914200	Weak transcription	Fetal Brain Male	brain
24	chr3:49911000-49911200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:49911000-49911400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:49911000-49914200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:49911000-49917200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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