Variant report

Variant	rs28573859
Chromosome Location	chr8:55064281-55064282
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:55048621..55051389-chr8:55064149..55065674,2	MCF-7	breast:
2	chr8:55012232..55015363-chr8:55063151..55067460,5	K562	blood:
3	chr8:55012350..55016130-chr8:55063151..55067016,6	K562	blood:
4	chr8:55046961..55051250-chr8:55057827..55066628,8	K562	blood:

Variant related genes	Relation type
ENSG00000137547	Chromatin interaction
ENSG00000120992	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10216491	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1039926	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10504161	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10958396	0.84[EUR][1000 genomes]
rs10958397	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11984645	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11984672	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11991952	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11993959	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11994629	0.84[EUR][1000 genomes]
rs11996128	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12114043	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12114739	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12679103	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12679542	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13276927	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13277185	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16919782	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16919784	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1828835	0.84[EUR][1000 genomes]
rs2008122	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271567	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292589	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292590	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2375696	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34168614	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34997387	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4737479	0.84[EUR][1000 genomes]
rs4737485	0.84[EUR][1000 genomes]
rs4737486	0.84[EUR][1000 genomes]
rs4737487	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4737488	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4738678	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58387069	0.84[EUR][1000 genomes]
rs58948369	0.82[EUR][1000 genomes]
rs60183530	0.85[EUR][1000 genomes]
rs61213253	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs61271559	0.85[EUR][1000 genomes]
rs61477279	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6473909	0.84[EUR][1000 genomes]
rs6473911	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6473913	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6473914	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6473915	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6983694	0.85[EUR][1000 genomes]
rs7011379	0.84[EUR][1000 genomes]
rs7011430	0.85[EUR][1000 genomes]
rs7012031	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71517558	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72614666	0.85[EUR][1000 genomes]
rs72614667	0.84[EUR][1000 genomes]
rs72614668	0.84[EUR][1000 genomes]
rs72614670	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72614671	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7830051	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7842911	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs952194	0.82[EUR][1000 genomes]
rs981638	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023983	chr8:54790309-55145770	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv539623	chr8:54790309-55145770	Bivalent Enhancer Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1026869	chr8:54989732-55089360	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28573859	MRPL15	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:55048600-55065600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:55048600-55066200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr8:55049000-55065800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr8:55049200-55064600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr8:55049400-55064600	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr8:55052600-55065600	Weak transcription	Fetal Heart	heart
7	chr8:55054600-55064800	Strong transcription	Fetal Intestine Small	intestine
8	chr8:55055200-55064600	Strong transcription	Fetal Muscle Leg	muscle
9	chr8:55055400-55064400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr8:55055400-55064400	Strong transcription	Brain Germinal Matrix	brain
11	chr8:55056800-55065600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr8:55057800-55066200	Weak transcription	Colonic Mucosa	Colon
13	chr8:55058800-55065800	Weak transcription	Small Intestine	intestine
14	chr8:55058800-55066200	Weak transcription	Psoas Muscle	Psoas
15	chr8:55060800-55065400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr8:55060800-55065600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr8:55061000-55066200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr8:55061400-55065000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr8:55061400-55065000	Weak transcription	Hela-S3	cervix
20	chr8:55061400-55065400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr8:55061400-55065600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr8:55061400-55065600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr8:55061600-55064600	Weak transcription	Aorta	Aorta
24	chr8:55061600-55065000	Weak transcription	Osteobl	bone
25	chr8:55061600-55065200	Weak transcription	Brain Angular Gyrus	brain
26	chr8:55061600-55065600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr8:55061600-55065600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr8:55061600-55065600	Weak transcription	HSMMtube	muscle
29	chr8:55061600-55065800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr8:55061600-55065800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr8:55061600-55065800	Weak transcription	Pancreas	Pancrea
32	chr8:55061600-55065800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr8:55061600-55065800	Weak transcription	Right Ventricle	heart
34	chr8:55061600-55065800	Weak transcription	Spleen	Spleen
35	chr8:55061600-55066800	Weak transcription	Esophagus	oesophagus
36	chr8:55061600-55078000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr8:55061600-55078400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr8:55061800-55064400	Weak transcription	Primary B cells from cord blood	blood
39	chr8:55061800-55065000	Weak transcription	NHDF-Ad	bronchial
40	chr8:55061800-55065600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr8:55061800-55065600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr8:55061800-55066000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr8:55062000-55065400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr8:55062200-55078400	Weak transcription	Right Atrium	heart
45	chr8:55062400-55068400	Enhancers	HUVEC	blood vessel
46	chr8:55062600-55064400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr8:55063000-55066600	Enhancers	Placenta	Placenta
48	chr8:55063000-55067200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr8:55063200-55064400	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr8:55063200-55064400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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