Variant report

Variant	rs12646890
Chromosome Location	chr4:57355262-57355263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57351584..57356949-chr4:57358180..57362673,6	MCF-7	breast:
2	chr4:57341371..57344122-chr4:57353182..57355439,2	K562	blood:
3	chr4:57345865..57348300-chr4:57353510..57355906,2	K562	blood:
4	chr4:57348088..57349910-chr4:57354539..57356063,2	K562	blood:
5	chr4:57353455..57355932-chr4:57360077..57362846,3	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10008223	0.80[ASN][1000 genomes]
rs10013402	0.82[ASN][1000 genomes]
rs10017460	0.81[ASN][1000 genomes]
rs10051	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10434444	0.83[ASN][1000 genomes]
rs10434445	0.80[ASN][1000 genomes]
rs1060472	0.83[ASN][1000 genomes]
rs11133442	0.89[ASN][1000 genomes]
rs12501334	0.83[ASN][1000 genomes]
rs12503412	0.83[ASN][1000 genomes]
rs12505767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12505939	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12508008	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12509542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510712	0.85[ASN][1000 genomes]
rs12511770	0.91[ASN][1000 genomes]
rs12513091	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs14211	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1474179	0.92[ASN][1000 genomes]
rs17086696	0.82[ASN][1000 genomes]
rs17086794	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17086832	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17086853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967559	0.89[ASN][1000 genomes]
rs1983378	0.83[ASN][1000 genomes]
rs2030366	0.83[ASN][1000 genomes]
rs28510634	0.80[ASN][1000 genomes]
rs28866881	0.83[ASN][1000 genomes]
rs4340842	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4346704	0.91[ASN][1000 genomes]
rs4618376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864579	0.82[ASN][1000 genomes]
rs4864580	0.82[ASN][1000 genomes]
rs4864583	0.83[ASN][1000 genomes]
rs4864585	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4865092	0.84[ASN][1000 genomes]
rs4865103	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4865107	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4865108	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5010012	0.80[ASN][1000 genomes]
rs55915354	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56040009	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56099714	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56229630	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56392224	0.83[ASN][1000 genomes]
rs56887793	0.84[ASN][1000 genomes]
rs58151706	0.82[ASN][1000 genomes]
rs58333131	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6554358	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66858948	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66863699	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820314	0.83[ASN][1000 genomes]
rs6821301	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6824893	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6829250	0.83[ASN][1000 genomes]
rs6832797	0.81[ASN][1000 genomes]
rs6834696	0.85[ASN][1000 genomes]
rs6849183	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7664841	0.94[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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12646890	SRP72	cis	Whole Blood	GTEx
rs12646890	SRP72	cis	Adipose Subcutaneous	GTEx
rs12646890	SRP72	Cis_1M	lymphoblastoid	RTeQTL
rs12646890	PPAT	Cis_1M	lymphoblastoid	RTeQTL
rs12646890	SRP72	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57334800-57364000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:57334800-57371200	Weak transcription	Stomach Mucosa	stomach
3	chr4:57335200-57371400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:57335600-57370200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr4:57335800-57359000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr4:57335800-57365600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:57335800-57369200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:57335800-57370200	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:57335800-57370800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:57336000-57362200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:57336000-57362600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:57336000-57364200	Strong transcription	Osteobl	bone
13	chr4:57336000-57369400	Strong transcription	Liver	Liver
14	chr4:57336000-57369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:57336000-57370000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:57336000-57370000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr4:57336000-57370200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:57336000-57371000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:57336200-57365000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr4:57336200-57369200	Strong transcription	Fetal Thymus	thymus
21	chr4:57336200-57370000	Strong transcription	Placenta	Placenta
22	chr4:57336200-57370400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:57336400-57364800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr4:57336400-57365400	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr4:57336400-57368200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr4:57336400-57369200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:57336400-57369200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:57336400-57370200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:57336600-57360400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:57336600-57364200	Strong transcription	Dnd41	blood
31	chr4:57336600-57365400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr4:57336600-57369200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr4:57337200-57363800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr4:57337200-57365400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr4:57337200-57369200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr4:57337400-57359000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr4:57337600-57358400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr4:57337600-57364000	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr4:57337600-57364800	Strong transcription	Fetal Intestine Large	intestine
40	chr4:57337800-57358000	Strong transcription	Fetal Lung	lung
41	chr4:57337800-57362400	Strong transcription	Primary B cells from cord blood	blood
42	chr4:57337800-57363200	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr4:57337800-57365600	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr4:57337800-57369200	Strong transcription	Adipose Nuclei	Adipose
45	chr4:57337800-57369400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr4:57338000-57365000	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr4:57338200-57364200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr4:57340600-57366600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:57340800-57356800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr4:57340800-57369000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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