Variant report

Variant	rs1317154
Chromosome Location	chr3:49910084-49910085
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49900314..49905841-chr3:49909576..49913570,6	K562	blood:
2	chr3:49908054..49910878-chr3:49916403..49919498,3	K562	blood:
3	chr3:49908717..49910264-chr3:49922246..49924394,2	MCF-7	breast:
4	chr3:49909687..49911283-chr3:49915526..49917285,2	K562	blood:
5	chr3:49894189..49896710-chr3:49908532..49911054,2	K562	blood:
6	chr3:49840589..49842616-chr3:49908973..49910773,2	K562	blood:

Variant related genes	Relation type
ENSG00000264706	Chromatin interaction
ENSG00000185614	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1062633	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130224	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130226	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11130228	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11130229	0.85[ASN][1000 genomes]
rs11130233	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11130234	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11713193	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11925192	0.90[ASN][1000 genomes]
rs12485600	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12496973	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13060128	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2230590	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2252833	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2280406	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2353579	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2353586	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2353587	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2526751	0.83[AMR][1000 genomes]
rs2624843	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2624844	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2681778	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2681780	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2681781	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2777888	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2883057	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34080578	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35065728	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3733135	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3774733	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3774758	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4688689	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4688690	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4688755	0.83[AMR][1000 genomes]
rs4688756	0.90[ASN][1000 genomes]
rs4688757	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4688758	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs55751738	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62262093	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6446187	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6446189	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6765484	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6767381	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6771546	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6772095	0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6780731	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6792892	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6795703	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72942333	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7609971	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7613875	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7621026	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7621352	0.82[AMR][1000 genomes]
rs7628058	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7634084	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7635002	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9821433	0.89[ASN][1000 genomes]
rs9821675	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9843653	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9848497	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9853222	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9862795	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9866695	0.84[AMR][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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs1317154	RBM6	cis	Stomach	GTEx
rs1317154	RBM6	cis	Adipose Subcutaneous	GTEx
rs1317154	RBM6	cis	Nerve Tibial	GTEx
rs1317154	FAM212A	cis	Esophagus Mucosa	GTEx
rs1317154	RBM6	cis	Esophagus Mucosa	GTEx
rs1317154	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs1317154	RBM6	cis	lung	GTEx
rs1317154	RBM6	cis	Whole Blood	GTEx
rs1317154	RBM6	cis	Thyroid	GTEx
rs1317154	RBM6	cis	Artery Tibial	GTEx
rs1317154	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs1317154	RBM6	cis	Esophagus Muscularis	GTEx
rs1317154	RBM6	cis	Heart Left Ventricle	GTEx
rs1317154	RBM6	cis	Artery Aorta	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49906600-49910800	Enhancers	Fetal Brain Male	brain
2	chr3:49907600-49910800	Weak transcription	Gastric	stomach
3	chr3:49907800-49911000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:49907800-49911200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:49908000-49911200	Enhancers	Fetal Brain Female	brain
6	chr3:49908000-49913600	Enhancers	Fetal Intestine Large	intestine
7	chr3:49908200-49911600	Enhancers	Brain Anterior Caudate	brain
8	chr3:49908600-49911200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:49908600-49911400	Enhancers	Fetal Intestine Small	intestine
10	chr3:49908800-49911000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr3:49909000-49911000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:49909200-49910600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:49909400-49910800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:49909600-49910200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:49909600-49910400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:49909600-49910600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:49909600-49910600	Enhancers	HepG2	liver
18	chr3:49909600-49911000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:49909800-49911400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:49910000-49910200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:49910000-49910600	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr3:49910000-49911000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:49910000-49911000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:49910000-49911200	Enhancers	Brain Germinal Matrix	brain
25	chr3:49910000-49912400	Enhancers	Stomach Mucosa	stomach
26	chr3:49910000-49917200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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