Variant report

Variant	rs2234385
Chromosome Location	chr3:49846041-49846042
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	POLR2A	chr3:49845915-49846046	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr3:49845993-49846077	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49844713..49846618-chr3:49938018..49940554,2	K562	blood:
2	chr3:49838468..49840938-chr3:49845462..49847993,2	MCF-7	breast:

Variant related genes	Relation type
MIR5193	TF binding region
UBA7	TF binding region
ENSG00000185614	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10049413	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1049256	0.89[ASN][1000 genomes]
rs10865958	0.96[ASN][1000 genomes]
rs10865959	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130214	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130216	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130218	0.87[ASN][1000 genomes]
rs11130219	0.87[ASN][1000 genomes]
rs11130221	0.89[ASN][1000 genomes]
rs1128535	0.96[ASN][1000 genomes]
rs11709680	0.87[ASN][1000 genomes]
rs11710675	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11714957	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11715304	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11716575	0.87[ASN][1000 genomes]
rs11717256	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11717463	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11920900	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12381242	0.87[ASN][1000 genomes]
rs12490656	0.84[ASN][1000 genomes]
rs12496226	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13063621	0.89[ASN][1000 genomes]
rs13084243	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13085679	0.96[ASN][1000 genomes]
rs13086130	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13086465	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13090611	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1317140	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13316065	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1491986	0.87[ASN][1000 genomes]
rs1799843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1799845	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234391	0.94[ASN][1000 genomes]
rs2246832	0.94[ASN][1000 genomes]
rs2247036	0.94[ASN][1000 genomes]
rs2271960	0.94[ASN][1000 genomes]
rs2271961	0.94[ASN][1000 genomes]
rs2276864	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291542	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2307021	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2352967	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2352974	0.94[ASN][1000 genomes]
rs2352975	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34451146	0.89[ASN][1000 genomes]
rs34522271	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34614773	0.87[ASN][1000 genomes]
rs34735338	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35210174	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35261599	0.92[ASN][1000 genomes]
rs35474403	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3749237	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3749240	0.89[ASN][1000 genomes]
rs3749241	0.89[ASN][1000 genomes]
rs3811695	0.85[ASN][1000 genomes]
rs3811696	0.87[ASN][1000 genomes]
rs3819325	0.90[ASN][1000 genomes]
rs4519692	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4768	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4855841	0.84[ASN][1000 genomes]
rs4855850	0.87[ASN][1000 genomes]
rs4855862	0.87[ASN][1000 genomes]
rs4855867	0.87[ASN][1000 genomes]
rs57648519	0.89[ASN][1000 genomes]
rs59906301	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60205400	0.89[ASN][1000 genomes]
rs62260715	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62260719	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260729	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6446295	0.92[ASN][1000 genomes]
rs6766836	0.89[ASN][1000 genomes]
rs6775384	0.96[ASN][1000 genomes]
rs6785549	0.85[ASN][1000 genomes]
rs6802890	0.89[ASN][1000 genomes]
rs6804655	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs695238	0.96[ASN][1000 genomes]
rs71324996	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7372725	0.83[ASN][1000 genomes]
rs7372730	0.85[ASN][1000 genomes]
rs7372966	0.83[ASN][1000 genomes]
rs7374183	0.83[ASN][1000 genomes]
rs7374277	0.83[ASN][1000 genomes]
rs7429353	0.83[ASN][1000 genomes]
rs7431078	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7431106	0.89[ASN][1000 genomes]
rs7618501	0.91[ASN][1000 genomes]
rs7618519	0.92[ASN][1000 genomes]
rs7629936	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7634886	0.87[ASN][1000 genomes]
rs7634902	0.89[ASN][1000 genomes]
rs7645061	0.96[ASN][1000 genomes]
rs7648987	0.96[ASN][1000 genomes]
rs7649348	0.92[ASN][1000 genomes]
rs9814765	0.87[ASN][1000 genomes]
rs9815766	0.89[ASN][1000 genomes]
rs9819511	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9850465	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9853458	0.87[ASN][1000 genomes]
rs9855505	0.83[ASN][1000 genomes]
rs9859153	0.89[ASN][1000 genomes]
rs9865480	0.87[ASN][1000 genomes]
rs9871654	0.88[ASN][1000 genomes]
rs9872864	0.83[ASN][1000 genomes]
rs9873183	0.83[ASN][1000 genomes]
rs9876508	0.92[ASN][1000 genomes]
rs9882639	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv967270	chr3:49845381-49870409	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2234385	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs2234385	WDR6	cis	Whole Blood	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49841400-49846400	Weak transcription	Ovary	ovary
2	chr3:49841400-49847000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr3:49841600-49846200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:49841600-49850400	Weak transcription	Small Intestine	intestine
5	chr3:49842000-49850600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:49842200-49846600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr3:49843400-49846200	Enhancers	Fetal Heart	heart
8	chr3:49843400-49846400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:49843400-49866400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:49843600-49846400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:49843600-49846400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:49843600-49846400	Weak transcription	Aorta	Aorta
13	chr3:49843600-49846400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr3:49843600-49846400	Weak transcription	Osteobl	bone
15	chr3:49843600-49846600	Enhancers	Primary hematopoietic stem cells	blood
16	chr3:49843600-49846800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:49843600-49850400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:49843600-49850600	Weak transcription	HSMM	muscle
19	chr3:49843600-49850800	Weak transcription	Psoas Muscle	Psoas
20	chr3:49844000-49847600	Genic enhancers	Fetal Thymus	thymus
21	chr3:49844000-49850200	Weak transcription	NHDF-Ad	bronchial
22	chr3:49844200-49846800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:49844200-49846800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:49844200-49847000	Genic enhancers	Fetal Stomach	stomach
25	chr3:49844400-49846400	Enhancers	K562	blood
26	chr3:49844400-49850200	Genic enhancers	Spleen	Spleen
27	chr3:49844800-49846400	Genic enhancers	Placenta	Placenta
28	chr3:49844800-49846800	Weak transcription	Brain Anterior Caudate	brain
29	chr3:49844800-49847400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:49844800-49849400	Strong transcription	Duodenum Mucosa	Duodenum
31	chr3:49845000-49846400	Enhancers	Primary B cells from cord blood	blood
32	chr3:49845000-49846600	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr3:49845000-49847000	Genic enhancers	Liver	Liver
34	chr3:49845000-49849600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:49845000-49850600	Genic enhancers	Primary B cells from peripheral blood	blood
36	chr3:49845000-49850600	Weak transcription	NH-A	brain
37	chr3:49845200-49846200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
38	chr3:49845200-49846200	Weak transcription	Thymus	Thymus
39	chr3:49845200-49846400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:49845200-49846400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr3:49845200-49847800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr3:49845200-49848600	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr3:49845200-49850000	Strong transcription	Colonic Mucosa	Colon
44	chr3:49845400-49846200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:49845400-49846200	Weak transcription	Fetal Intestine Large	intestine
46	chr3:49845400-49846400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:49845400-49846800	Weak transcription	NHLF	lung
48	chr3:49845400-49847000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:49845400-49847800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:49845400-49849600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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