Variant report

Variant	rs12381242
Chromosome Location	chr3:49746819-49746820
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49744683..49746856-chr3:49748059..49750371,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164068	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10049413	0.84[ASN][1000 genomes]
rs1049256	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10865958	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10865959	0.84[ASN][1000 genomes]
rs11130214	0.94[ASN][1000 genomes]
rs11130216	0.94[ASN][1000 genomes]
rs11130218	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130219	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130221	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1128535	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11709680	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710675	0.96[ASN][1000 genomes]
rs11714957	0.94[ASN][1000 genomes]
rs11715304	0.88[ASN][1000 genomes]
rs11716575	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717256	0.89[ASN][1000 genomes]
rs11717463	0.94[ASN][1000 genomes]
rs11920900	0.93[ASN][1000 genomes]
rs12490656	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12496226	0.89[ASN][1000 genomes]
rs13063621	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13084243	0.94[ASN][1000 genomes]
rs13085679	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13086130	0.94[ASN][1000 genomes]
rs13086465	0.92[ASN][1000 genomes]
rs13090611	0.86[ASN][1000 genomes]
rs1317140	0.80[ASN][1000 genomes]
rs13316065	0.85[ASN][1000 genomes]
rs1491986	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1799843	0.87[ASN][1000 genomes]
rs1799845	0.87[ASN][1000 genomes]
rs2234385	0.87[ASN][1000 genomes]
rs2234391	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2246832	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2247036	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271960	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271961	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2276864	0.84[ASN][1000 genomes]
rs2291542	0.96[ASN][1000 genomes]
rs2307021	0.96[ASN][1000 genomes]
rs2352967	0.85[ASN][1000 genomes]
rs2352974	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2352975	0.84[ASN][1000 genomes]
rs34451146	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34522271	0.94[ASN][1000 genomes]
rs34614773	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34735338	0.92[ASN][1000 genomes]
rs35210174	0.94[ASN][1000 genomes]
rs35261599	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35474403	0.94[ASN][1000 genomes]
rs3749237	0.94[ASN][1000 genomes]
rs3749240	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3749241	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3811695	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3811696	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3819325	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4519692	0.80[ASN][1000 genomes]
rs4768	0.96[ASN][1000 genomes]
rs4855841	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4855850	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4855862	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855867	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57648519	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59906301	0.89[ASN][1000 genomes]
rs60205400	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62260715	0.92[ASN][1000 genomes]
rs62260719	0.87[ASN][1000 genomes]
rs62260729	0.84[ASN][1000 genomes]
rs6446295	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6766836	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6775384	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6785549	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6802890	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6804655	0.94[ASN][1000 genomes]
rs695238	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7372725	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7372730	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7372966	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7374183	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7374277	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7426497	0.86[AMR][1000 genomes]
rs7429353	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7431078	0.94[ASN][1000 genomes]
rs7431106	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7618501	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7618519	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7629936	0.86[ASN][1000 genomes]
rs7634886	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7634902	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7645061	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7648987	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7649348	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9814765	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9815766	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9819511	0.84[ASN][1000 genomes]
rs9850465	0.84[ASN][1000 genomes]
rs9853458	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9855505	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9859153	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9865480	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9871654	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9872864	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9873183	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9876508	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9882639	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[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	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	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
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1796605	chr3:49744556-49760567	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12381242	FAM212A	cis	Esophagus Mucosa	GTEx
rs12381242	RBM6	cis	Esophagus Muscularis	GTEx
rs12381242	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs12381242	RBM6	cis	Thyroid	GTEx
rs12381242	RBM6	cis	lung	GTEx
rs12381242	UBA7	cis	Whole Blood	GTEx
rs12381242	RBM6	cis	Artery Tibial	GTEx
rs12381242	RBM6	cis	Whole Blood	GTEx
rs12381242	UBA7	cis	Esophagus Mucosa	GTEx
rs12381242	RBM6	cis	Nerve Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49728000-49748800	Weak transcription	A549	lung
2	chr3:49728400-49753200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:49728400-49756600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:49728600-49750400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr3:49729200-49749800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:49729200-49750200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:49729200-49755800	Weak transcription	Right Atrium	heart
8	chr3:49729400-49750200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:49732200-49755000	Strong transcription	Fetal Intestine Small	intestine
10	chr3:49733000-49750200	Weak transcription	Psoas Muscle	Psoas
11	chr3:49734400-49756000	Strong transcription	Liver	Liver
12	chr3:49735400-49755400	Weak transcription	Stomach Mucosa	stomach
13	chr3:49736000-49749800	Weak transcription	GM12878-XiMat	blood
14	chr3:49736000-49753000	Weak transcription	K562	blood
15	chr3:49736800-49756400	Weak transcription	HSMM	muscle
16	chr3:49739000-49752000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:49739000-49756400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:49739200-49753200	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:49740000-49755600	Weak transcription	Fetal Brain Male	brain
20	chr3:49740200-49756000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:49740200-49756600	Weak transcription	HSMMtube	muscle
22	chr3:49740400-49747400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:49740400-49755000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:49740600-49759800	Weak transcription	Hela-S3	cervix
25	chr3:49740800-49756400	Weak transcription	Osteobl	bone
26	chr3:49741400-49755200	Strong transcription	Placenta	Placenta
27	chr3:49741800-49755600	Weak transcription	HUVEC	blood vessel
28	chr3:49742200-49750000	Weak transcription	Fetal Lung	lung
29	chr3:49742600-49756200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:49743000-49750200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:49743000-49756400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:49743000-49756800	Weak transcription	Small Intestine	intestine
33	chr3:49743200-49751400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:49743400-49756200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:49743600-49753200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:49743600-49753200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:49743800-49751400	Weak transcription	NHLF	lung
38	chr3:49743800-49755800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr3:49744000-49748200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:49744000-49749000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:49744000-49750200	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:49744000-49750400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:49744000-49752800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:49744000-49755400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr3:49744000-49756400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:49744200-49752800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:49744200-49753200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:49744400-49750200	Weak transcription	Primary B cells from peripheral blood	blood
49	chr3:49744600-49748600	Weak transcription	Fetal Muscle Trunk	muscle
50	chr3:49744600-49749600	Weak transcription	Primary T cells fromperipheralblood	blood

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