Variant report

Variant	rs4894350
Chromosome Location	chr3:138498986-138498987
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:138497768..138501036-chr3:138504474..138507070,3	MCF-7	breast:
2	chr3:138497639..138499838-chr3:138521505..138523466,2	K562	blood:
3	chr3:138491707..138493497-chr3:138496731..138499014,2	K562	blood:
4	chr3:138491707..138493497-chr3:138496731..138499046,3	K562	blood:

Extended variants
information (count: 153 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs1066197	0.90[EUR][1000 genomes]
rs1068104	0.91[EUR][1000 genomes]
rs1068685	0.91[EUR][1000 genomes]
rs11705762	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709768	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713049	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717457	0.89[EUR][1000 genomes]
rs11720178	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924814	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13069296	0.92[EUR][1000 genomes]
rs13082808	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13433948	0.88[EUR][1000 genomes]
rs1400266	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1663554	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1663556	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1673597	0.91[EUR][1000 genomes]
rs168633	0.96[EUR][1000 genomes]
rs181729	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs187245	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191713	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191714	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191775	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2197387	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348147	0.85[EUR][1000 genomes]
rs244380	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs244381	0.94[EUR][1000 genomes]
rs2595928	0.89[EUR][1000 genomes]
rs2595930	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2595932	1.00[ASN][1000 genomes]
rs2607108	0.89[ASN][1000 genomes]
rs2607109	0.89[ASN][1000 genomes]
rs2607796	0.90[EUR][1000 genomes]
rs28376988	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28408150	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2881900	0.81[EUR][1000 genomes]
rs34900559	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35214574	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361054	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361055	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs361056	1.00[ASN][1000 genomes]
rs361057	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs361059	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361060	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361061	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs361062	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361063	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361064	1.00[ASN][1000 genomes]
rs361065	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs361066	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361067	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361068	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361069	0.89[EUR][1000 genomes]
rs361071	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361072	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361079	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361080	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361081	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361082	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361083	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361084	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361085	0.89[ASN][1000 genomes]
rs361088	0.91[EUR][1000 genomes]
rs361089	0.91[EUR][1000 genomes]
rs361092	0.92[EUR][1000 genomes]
rs361094	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361096	1.00[ASN][1000 genomes]
rs361097	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs371762	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs385254	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398065	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404110	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs409507	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413147	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs425901	0.94[EUR][1000 genomes]
rs4305444	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439720	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4405948	0.80[EUR][1000 genomes]
rs448808	0.93[EUR][1000 genomes]
rs470359	0.92[EUR][1000 genomes]
rs473388	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475254	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs476800	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs482334	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894351	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894352	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894353	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894354	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491371	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs493152	1.00[ASN][1000 genomes]
rs497900	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500687	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511207	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs524164	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531577	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs539156	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs539619	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540198	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540907	0.95[EUR][1000 genomes]
rs550768	0.91[EUR][1000 genomes]
rs558905	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559160	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs559451	0.95[EUR][1000 genomes]
rs564455	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574942	1.00[ASN][1000 genomes]
rs589986	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603723	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs607044	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618457	0.89[EUR][1000 genomes]
rs621204	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62282169	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624099	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs625468	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs635592	0.91[EUR][1000 genomes]
rs6439817	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439819	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs647972	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs654459	0.84[EUR][1000 genomes]
rs6776585	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781914	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6784610	0.84[EUR][1000 genomes]
rs6794270	0.85[EUR][1000 genomes]
rs6795203	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6801207	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810351	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7612106	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643722	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772612	0.98[EUR][1000 genomes]
rs773045	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs773184	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9818354	0.82[EUR][1000 genomes]
rs9821694	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822714	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823213	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9832012	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834963	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853819	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9863481	0.84[EUR][1000 genomes]
rs9864176	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874723	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877108	0.84[EUR][1000 genomes]
rs9879784	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1010514	chr3:138365640-138737688	Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv1000927	chr3:138423543-138632596	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv917964	chr3:138440701-138699084	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv967071	chr3:138496873-138501049	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4894350	PIK3CB	Cis_1M	lymphoblastoid	RTeQTL
rs4894350	CEP70	Cis_1M	lymphoblastoid	RTeQTL
rs4894350	FAIM	cis	Muscle Skeletal	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138393800-138515000	Weak transcription	Aorta	Aorta
2	chr3:138408400-138499200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:138488000-138499800	Weak transcription	Thymus	Thymus
4	chr3:138488000-138504600	Weak transcription	Primary B cells from cord blood	blood
5	chr3:138488000-138519200	Weak transcription	Spleen	Spleen
6	chr3:138488200-138499600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr3:138488200-138499600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:138488200-138503200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:138488400-138512200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:138489000-138511600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr3:138489200-138499200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:138489200-138500000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:138489200-138519200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:138489800-138499000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr3:138489800-138499200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr3:138490200-138499200	Weak transcription	Dnd41	blood
17	chr3:138490800-138499200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:138490800-138499400	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:138492400-138515800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:138494200-138505600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:138494400-138499600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:138494400-138500200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:138494400-138511600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:138494400-138511600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:138494600-138499600	Weak transcription	Fetal Thymus	thymus
26	chr3:138494600-138499800	Weak transcription	Colonic Mucosa	Colon
27	chr3:138494600-138499800	Weak transcription	Stomach Mucosa	stomach
28	chr3:138494600-138504400	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr3:138494600-138510200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr3:138494600-138510200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:138494600-138510200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:138494600-138511000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:138494600-138512200	Weak transcription	Esophagus	oesophagus
34	chr3:138494600-138513000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:138494600-138513600	Weak transcription	HSMM	muscle
36	chr3:138494600-138515800	Weak transcription	Ovary	ovary
37	chr3:138494600-138518600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:138494600-138521200	Weak transcription	Right Ventricle	heart
39	chr3:138494800-138499400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:138494800-138501200	Weak transcription	Fetal Heart	heart
41	chr3:138494800-138510200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr3:138494800-138537000	Weak transcription	HUVEC	blood vessel
43	chr3:138495000-138499400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:138495400-138505000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:138495400-138506200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:138495600-138505200	Weak transcription	Osteobl	bone
47	chr3:138495600-138505400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:138495600-138505600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:138495600-138505600	Weak transcription	Adipose Nuclei	Adipose
50	chr3:138495600-138505600	Weak transcription	HMEC	breast

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