Variant report

Variant	rs12679103
Chromosome Location	chr8:55059927-55059928
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:55011657..55013589-chr8:55059186..55062088,2	K562	blood:
2	chr8:55057740..55060446-chr8:55064818..55067439,2	K562	blood:
3	chr8:54933508..54935660-chr8:55057965..55060583,2	K562	blood:
4	chr8:55059314..55060958-chr8:55064312..55066483,2	MCF-7	breast:
5	chr8:55053583..55055531-chr8:55058324..55060040,2	K562	blood:
6	chr8:55046961..55051250-chr8:55057827..55066628,8	K562	blood:
7	chr8:55059169..55061201-chr8:55073934..55076010,2	K562	blood:

Variant related genes	Relation type
ENSG00000137547	Chromatin interaction
ENSG00000187735	Chromatin interaction
ENSG00000251835	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10216491	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1039926	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10504161	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10958396	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10958397	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11984645	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11984672	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11991952	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11993959	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11994629	0.90[EUR][1000 genomes]
rs11996128	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12114043	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12114739	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12674895	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12679542	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13276927	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13277185	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16919782	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16919784	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1828835	0.90[EUR][1000 genomes]
rs2008122	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2271567	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2292589	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2292590	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2375696	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28573859	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34168614	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34997387	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4737479	0.90[EUR][1000 genomes]
rs4737485	0.90[EUR][1000 genomes]
rs4737486	0.90[EUR][1000 genomes]
rs4738678	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58387069	0.90[EUR][1000 genomes]
rs58948369	0.88[EUR][1000 genomes]
rs61213253	0.80[EUR][1000 genomes]
rs61477279	0.81[EUR][1000 genomes]
rs6473911	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6473913	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6473914	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6473915	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7012031	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71517558	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72614667	0.90[EUR][1000 genomes]
rs72614668	0.92[EUR][1000 genomes]
rs72614670	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72614671	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7830051	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7842911	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs952194	0.89[EUR][1000 genomes]
rs981638	0.87[AMR][1000 genomes];0.94[EUR][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
rs12679103	MRPL15	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 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	chr8:55048800-55063200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr8:55049000-55061800	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr8:55049000-55062000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr8:55049000-55065800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr8:55049200-55061600	Strong transcription	Osteobl	bone
8	chr8:55049200-55063800	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr8:55049200-55063800	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr8:55049200-55064000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr8:55049200-55064000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr8:55049200-55064000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr8:55049200-55064000	Strong transcription	Fetal Intestine Large	intestine
14	chr8:55049200-55064200	Strong transcription	Fetal Muscle Trunk	muscle
15	chr8:55049200-55064600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr8:55049400-55061600	Strong transcription	Stomach Smooth Muscle	stomach
17	chr8:55049400-55063600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr8:55049400-55063800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr8:55049400-55064000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr8:55049400-55064000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr8:55049400-55064000	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr8:55049400-55064600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr8:55049600-55062000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr8:55049600-55064000	Strong transcription	Adipose Nuclei	Adipose
25	chr8:55049800-55063600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr8:55049800-55064000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr8:55050000-55063000	Strong transcription	HMEC	breast
28	chr8:55050000-55063800	Strong transcription	Duodenum Mucosa	Duodenum
29	chr8:55050600-55063800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr8:55052000-55061600	Strong transcription	NH-A	brain
31	chr8:55052000-55061800	Strong transcription	K562	blood
32	chr8:55052200-55061400	Strong transcription	Hela-S3	cervix
33	chr8:55052200-55061800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr8:55052200-55063200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr8:55052400-55061600	Strong transcription	NHEK	skin
36	chr8:55052600-55062200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr8:55052600-55063200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr8:55052600-55065600	Weak transcription	Fetal Heart	heart
39	chr8:55053600-55060800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr8:55053600-55061400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr8:55053600-55061400	Strong transcription	NHLF	lung
42	chr8:55053600-55061800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr8:55053600-55061800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr8:55053600-55061800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr8:55053600-55063000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr8:55053600-55063800	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr8:55053600-55064000	Strong transcription	Fetal Thymus	thymus
48	chr8:55053800-55062800	Strong transcription	Placenta	Placenta
49	chr8:55054600-55062800	Strong transcription	Fetal Stomach	stomach
50	chr8:55054600-55063200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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