Variant report

Variant	rs58657577
Chromosome Location	chr16:75668768-75668769
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	chr16:75661594..75664280-chr16:75668715..75671473,2	MCF-7	breast:
2	chr16:75666708..75668853-chr16:75672275..75674428,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000065427	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10163345	0.85[EUR][1000 genomes]
rs10468346	1.00[ASN][1000 genomes]
rs11546854	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11860980	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11862453	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11864677	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11866252	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16941008	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16942022	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16942809	0.83[EUR][1000 genomes]
rs16942870	0.83[EUR][1000 genomes]
rs1865492	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1991052	0.83[EUR][1000 genomes]
rs2233803	0.96[EUR][1000 genomes]
rs2233805	0.96[EUR][1000 genomes]
rs2233810	0.96[EUR][1000 genomes]
rs28571860	1.00[ASN][1000 genomes]
rs56892159	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58000098	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58996069	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59624897	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59794444	1.00[EUR][1000 genomes]
rs60376290	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60415088	0.94[EUR][1000 genomes]
rs60545422	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60664312	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61588474	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62619985	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186790	0.94[EUR][1000 genomes]
rs7193257	0.96[EUR][1000 genomes]
rs7195089	0.94[EUR][1000 genomes]
rs73613267	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73613272	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73615089	0.94[EUR][1000 genomes]
rs8051771	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9989360	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv532562	chr16:75614947-76371158	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1062010	chr16:75628562-75825725	Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1064880	chr16:75628562-75895699	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats 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	43 gene(s)	inside rSNPs	diseases
6	nsv542960	chr16:75628562-75895699	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv1065543	chr16:75631306-75800170	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58657577	KARS	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75658400-75679200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr16:75658400-75679800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:75658400-75679800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr16:75658600-75678200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr16:75658800-75672400	Strong transcription	Fetal Brain Female	brain
6	chr16:75658800-75672600	Strong transcription	GM12878-XiMat	blood
7	chr16:75658800-75677000	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr16:75658800-75679800	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr16:75659000-75671800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr16:75659000-75672000	Strong transcription	Skeletal Muscle Male	skeletal muscle
11	chr16:75659000-75677000	Strong transcription	Brain Substantia Nigra	brain
12	chr16:75659000-75678200	Strong transcription	Fetal Muscle Leg	muscle
13	chr16:75659000-75678400	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr16:75659200-75675600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr16:75659200-75678000	Strong transcription	HepG2	liver
16	chr16:75659200-75680000	Strong transcription	Fetal Stomach	stomach
17	chr16:75659200-75680000	Strong transcription	A549	lung
18	chr16:75659200-75680600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr16:75659400-75670600	Strong transcription	Brain Cingulate Gyrus	brain
20	chr16:75659400-75671400	Strong transcription	Fetal Lung	lung
21	chr16:75659400-75671800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr16:75659400-75671800	Strong transcription	Brain Germinal Matrix	brain
23	chr16:75659400-75672400	Strong transcription	Ovary	ovary
24	chr16:75659400-75674200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr16:75659400-75676800	Strong transcription	Fetal Muscle Trunk	muscle
26	chr16:75659400-75677200	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr16:75659400-75678400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr16:75659400-75678400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr16:75659400-75679600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr16:75659400-75680000	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr16:75659600-75670400	Strong transcription	NHLF	lung
32	chr16:75659600-75671400	Strong transcription	Brain Anterior Caudate	brain
33	chr16:75659600-75671600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr16:75659600-75671600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr16:75659600-75671600	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr16:75659600-75672000	Strong transcription	Brain Angular Gyrus	brain
37	chr16:75659600-75672000	Strong transcription	NHEK	skin
38	chr16:75659600-75672400	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr16:75659600-75675600	Strong transcription	HMEC	breast
40	chr16:75659600-75676800	Strong transcription	Left Ventricle	heart
41	chr16:75659600-75677000	Strong transcription	Brain Hippocampus Middle	brain
42	chr16:75659600-75678200	Strong transcription	Duodenum Mucosa	Duodenum
43	chr16:75659600-75678200	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr16:75659600-75678200	Strong transcription	Fetal Intestine Large	intestine
45	chr16:75659600-75678400	Strong transcription	Primary B cells from peripheral blood	blood
46	chr16:75659600-75678600	Strong transcription	Liver	Liver
47	chr16:75659600-75678800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr16:75659600-75679200	Strong transcription	Stomach Smooth Muscle	stomach
49	chr16:75659600-75679400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr16:75659600-75679600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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