Variant report

Variant	rs28510634
Chromosome Location	chr4:57217050-57217051
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	chr4:57215250..57218405-chr4:57219428..57221610,3	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10008223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10010544	0.91[EUR][1000 genomes]
rs10013402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10017460	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10434444	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10434445	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10461357	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1060472	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11133442	0.85[ASN][1000 genomes]
rs1124569	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11723782	0.91[EUR][1000 genomes]
rs12498340	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12501334	0.93[ASN][1000 genomes]
rs12503412	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12508008	0.80[ASN][1000 genomes]
rs12509542	0.80[ASN][1000 genomes]
rs12510712	0.81[ASN][1000 genomes]
rs12511770	0.83[ASN][1000 genomes]
rs12512742	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12513091	0.80[ASN][1000 genomes]
rs12646890	0.80[ASN][1000 genomes]
rs1474179	0.88[ASN][1000 genomes]
rs17086696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086794	0.85[ASN][1000 genomes]
rs17086853	0.80[ASN][1000 genomes]
rs1967559	0.85[ASN][1000 genomes]
rs1983378	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2030366	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2049088	0.90[EUR][1000 genomes]
rs2271925	0.84[EUR][1000 genomes]
rs28866881	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3796548	0.84[EUR][1000 genomes]
rs4263445	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4340842	0.84[ASN][1000 genomes]
rs4346704	0.83[ASN][1000 genomes]
rs4618376	0.80[ASN][1000 genomes]
rs4864579	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864583	0.93[ASN][1000 genomes]
rs4865088	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4865089	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4865092	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4865103	0.82[ASN][1000 genomes]
rs4865107	0.80[ASN][1000 genomes]
rs5010012	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56066795	0.84[EUR][1000 genomes]
rs56099714	0.80[ASN][1000 genomes]
rs56392224	0.93[ASN][1000 genomes]
rs56887793	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58151706	0.92[ASN][1000 genomes]
rs59997251	0.87[EUR][1000 genomes]
rs61032900	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6554344	0.91[EUR][1000 genomes]
rs66858948	0.85[ASN][1000 genomes]
rs66863699	0.80[ASN][1000 genomes]
rs67957495	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6820279	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6820314	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6821301	0.86[ASN][1000 genomes]
rs6829250	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6832797	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6834696	0.95[ASN][1000 genomes]
rs6849183	0.86[ASN][1000 genomes]
rs7664841	0.86[ASN][1000 genomes]
rs7670991	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7696808	0.93[EUR][1000 genomes]
rs8340	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9799864	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv3415289	chr4:57063312-57236755	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	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
6	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28510634	SRP72	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57167800-57218600	Weak transcription	Small Intestine	intestine
2	chr4:57190600-57252400	Weak transcription	Colonic Mucosa	Colon
3	chr4:57195200-57238000	Weak transcription	HUVEC	blood vessel
4	chr4:57196000-57238200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:57202600-57221400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:57202800-57252400	Weak transcription	NHDF-Ad	bronchial
7	chr4:57203000-57252600	Weak transcription	Right Ventricle	heart
8	chr4:57203200-57235200	Weak transcription	Osteobl	bone
9	chr4:57203200-57251800	Weak transcription	A549	lung
10	chr4:57203400-57252400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr4:57203600-57229400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:57204000-57252200	Weak transcription	NH-A	brain
13	chr4:57204200-57222400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:57204200-57227200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:57204200-57252200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr4:57204800-57223400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:57204800-57235400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr4:57204800-57251800	Weak transcription	Fetal Brain Male	brain
19	chr4:57205000-57217200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr4:57205000-57223000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:57205000-57228000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr4:57205200-57228200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:57205200-57229200	Weak transcription	Brain Germinal Matrix	brain
24	chr4:57205400-57228000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:57207800-57253000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr4:57208800-57222800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr4:57210600-57222400	Weak transcription	Thymus	Thymus
28	chr4:57211000-57251600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr4:57211800-57217600	Strong transcription	Liver	Liver
30	chr4:57211800-57218400	Strong transcription	Primary hematopoietic stem cells	blood
31	chr4:57211800-57252200	Weak transcription	Fetal Heart	heart
32	chr4:57212000-57221000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr4:57212400-57251800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr4:57212800-57217600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:57213000-57244200	Weak transcription	Spleen	Spleen
36	chr4:57213200-57229200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr4:57213400-57251600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr4:57213400-57252200	Weak transcription	NHLF	lung
39	chr4:57213600-57222400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr4:57213600-57223200	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr4:57213600-57250200	Weak transcription	K562	blood
42	chr4:57213600-57252000	Weak transcription	HMEC	breast
43	chr4:57214400-57251800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr4:57214600-57252200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr4:57214800-57222400	Weak transcription	Lung	lung
46	chr4:57214800-57227800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr4:57214800-57229000	Weak transcription	Fetal Thymus	thymus
48	chr4:57215000-57218600	Weak transcription	Aorta	Aorta
49	chr4:57215000-57222400	Weak transcription	Gastric	stomach
50	chr4:57215000-57222800	Weak transcription	Esophagus	oesophagus

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