Variant report

Variant	rs6446295
Chromosome Location	chr3:49809063-49809064
allele	G/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	MEF2A	chr3:49808800-49809096	GM12878	blood:	n/a	n/a
2	RUNX3	chr3:49808744-49809166	GM12878	blood:	n/a	n/a
3	RUNX3	chr3:49808694-49809182	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49791928..49793924-chr3:49807160..49809101,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000244730	TF binding region

Extended variants
information (count: 107 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10049413	0.88[ASN][1000 genomes]
rs1049256	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10865958	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10865959	0.88[ASN][1000 genomes]
rs11130214	0.94[ASN][1000 genomes]
rs11130216	0.94[ASN][1000 genomes]
rs11130218	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130219	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130221	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1128535	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11709680	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11710675	0.96[ASN][1000 genomes]
rs11714957	0.99[ASN][1000 genomes]
rs11715304	0.90[ASN][1000 genomes]
rs11716575	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11717256	0.89[ASN][1000 genomes]
rs11717463	0.99[ASN][1000 genomes]
rs11920900	0.98[ASN][1000 genomes]
rs12381242	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12490656	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12496226	0.89[ASN][1000 genomes]
rs13063621	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13084243	0.99[ASN][1000 genomes]
rs13085679	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13086130	0.99[ASN][1000 genomes]
rs13086465	0.96[ASN][1000 genomes]
rs13090611	0.90[ASN][1000 genomes]
rs1317140	0.82[ASN][1000 genomes]
rs13316065	0.87[ASN][1000 genomes]
rs1491986	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1799843	0.92[ASN][1000 genomes]
rs1799845	0.92[ASN][1000 genomes]
rs2234385	0.92[ASN][1000 genomes]
rs2234391	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2246832	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2247036	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2271960	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2271961	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276864	0.88[ASN][1000 genomes]
rs2291542	0.96[ASN][1000 genomes]
rs2307021	0.96[ASN][1000 genomes]
rs2352967	0.87[ASN][1000 genomes]
rs2352974	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2352975	0.88[ASN][1000 genomes]
rs34451146	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34522271	0.99[ASN][1000 genomes]
rs34614773	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34735338	0.96[ASN][1000 genomes]
rs35210174	0.99[ASN][1000 genomes]
rs35261599	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35474403	0.99[ASN][1000 genomes]
rs3749237	0.99[ASN][1000 genomes]
rs3749240	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3749241	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3811695	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3811696	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3819325	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4519692	0.82[ASN][1000 genomes]
rs4768	0.96[ASN][1000 genomes]
rs4855841	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4855850	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4855862	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4855867	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57648519	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59906301	0.94[ASN][1000 genomes]
rs60205400	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62260715	0.96[ASN][1000 genomes]
rs62260719	0.92[ASN][1000 genomes]
rs62260729	0.88[ASN][1000 genomes]
rs6766836	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6775384	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6785549	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6802890	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6804655	0.94[ASN][1000 genomes]
rs695238	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71324996	0.82[ASN][1000 genomes]
rs7372725	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7372730	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7372966	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7374183	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7374277	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7426497	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7429353	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7431078	0.99[ASN][1000 genomes]
rs7431106	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7618501	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7618519	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629936	0.90[ASN][1000 genomes]
rs7634886	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7634902	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7645061	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7648987	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7649348	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814765	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9815766	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9819511	0.86[ASN][1000 genomes]
rs9850465	0.88[ASN][1000 genomes]
rs9853458	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9855505	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9859153	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9865480	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9871654	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9872864	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9873183	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9876508	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882639	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6446295	UBA7	cis	Whole Blood	GTEx
rs6446295	RBM6	cis	Whole Blood	GTEx
rs6446295	RBM6	cis	Thyroid	GTEx
rs6446295	RBM6	cis	Adipose Subcutaneous	GTEx
rs6446295	RBM6	cis	Artery Tibial	GTEx
rs6446295	RBM6	cis	Esophagus Muscularis	GTEx
rs6446295	FAM212A	cis	Esophagus Mucosa	GTEx
rs6446295	RBM6	cis	lung	GTEx
rs6446295	RBM6	cis	Nerve Tibial	GTEx
rs6446295	RBM6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49775600-49817000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr3:49775800-49810200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:49775800-49823000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:49776400-49812000	Weak transcription	HSMM	muscle
5	chr3:49776400-49812200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:49776400-49812600	Weak transcription	Gastric	stomach
7	chr3:49776400-49818000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:49776400-49818000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:49776400-49818200	Weak transcription	Fetal Kidney	kidney
10	chr3:49776600-49812000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:49782600-49814000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:49785600-49822400	Weak transcription	HSMMtube	muscle
13	chr3:49785600-49822600	Weak transcription	Esophagus	oesophagus
14	chr3:49785800-49811200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:49785800-49812400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:49785800-49818000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:49786000-49812400	Weak transcription	NHEK	skin
18	chr3:49786000-49812600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:49786000-49812800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:49786000-49814400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr3:49786000-49823000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:49786200-49812000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:49786200-49812600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:49786200-49812600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:49786200-49822400	Weak transcription	HMEC	breast
26	chr3:49786400-49817800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr3:49786600-49812800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:49786600-49817800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:49787800-49812600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr3:49787800-49812600	Weak transcription	Thymus	Thymus
31	chr3:49791400-49812000	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:49791800-49812400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:49792400-49812600	Weak transcription	Pancreas	Pancrea
34	chr3:49793800-49817600	Weak transcription	Spleen	Spleen
35	chr3:49795000-49818000	Weak transcription	Psoas Muscle	Psoas
36	chr3:49795000-49819000	Weak transcription	Right Ventricle	heart
37	chr3:49795000-49821000	Weak transcription	K562	blood
38	chr3:49795400-49822400	Weak transcription	Stomach Mucosa	stomach
39	chr3:49797200-49812600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:49797400-49812000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr3:49802400-49818000	Weak transcription	Right Atrium	heart
42	chr3:49802600-49810200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:49804000-49812800	Weak transcription	Liver	Liver
44	chr3:49804000-49822600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr3:49804200-49816000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:49805400-49812600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:49806200-49818800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:49806600-49819000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:49806800-49809200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:49806800-49809400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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