Variant report

Variant	rs56892159
Chromosome Location	chr16:75689900-75689901
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:75689891-75690066	MCF-7	breast:	n/a	n/a
2	POLR2A	chr16:75689815-75690089	GM12878	blood:	n/a	n/a
3	POLR2A	chr16:75689868-75690187	K562	blood:	n/a	n/a
4	POLR2A	chr16:75689624-75689977	HepG2	liver:	n/a	n/a
5	POLR2A	chr16:75689596-75689969	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:75688504..75690013-chr16:75704731..75707189,2	K562	blood:

Variant related genes	Relation type
TERF2IP	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10163345	0.83[EUR][1000 genomes]
rs10468346	1.00[ASN][1000 genomes]
rs1133766	0.84[EUR][1000 genomes]
rs11546854	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11640406	0.84[EUR][1000 genomes]
rs11640743	0.84[EUR][1000 genomes]
rs11641108	0.84[EUR][1000 genomes]
rs11646086	0.84[EUR][1000 genomes]
rs11646574	0.84[EUR][1000 genomes]
rs11648206	0.84[EUR][1000 genomes]
rs11649504	0.84[EUR][1000 genomes]
rs11649505	0.84[EUR][1000 genomes]
rs11649571	0.84[EUR][1000 genomes]
rs11860980	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11862453	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11864677	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11866252	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16941008	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16942022	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16942809	0.89[EUR][1000 genomes]
rs16942870	0.89[EUR][1000 genomes]
rs16943274	0.81[EUR][1000 genomes]
rs16943285	0.81[EUR][1000 genomes]
rs1865492	0.98[EUR][1000 genomes]
rs1991052	0.89[EUR][1000 genomes]
rs2233803	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2233805	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2233810	0.98[EUR][1000 genomes]
rs28571860	1.00[ASN][1000 genomes]
rs35135836	0.84[EUR][1000 genomes]
rs58000098	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58657577	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58996069	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59624897	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59794444	0.94[EUR][1000 genomes]
rs60376290	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60415088	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60545422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60664312	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61588474	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62619985	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186790	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7193257	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7195089	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73613267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73613272	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73615089	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8051771	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9989360	1.00[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
rs56892159	KARS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75683800-75691800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr16:75683800-75692800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:75684600-75695400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:75686200-75690400	Weak transcription	Psoas Muscle	Psoas
5	chr16:75686200-75694400	Weak transcription	Right Atrium	heart
6	chr16:75686400-75695800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr16:75686600-75695200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr16:75687000-75693000	Strong transcription	K562	blood
9	chr16:75687000-75695400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr16:75687400-75690400	Strong transcription	Fetal Intestine Small	intestine
11	chr16:75687400-75691400	Weak transcription	Fetal Heart	heart
12	chr16:75687400-75692600	Strong transcription	Thymus	Thymus
13	chr16:75687400-75692800	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr16:75687400-75693000	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr16:75687400-75693600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr16:75687400-75696000	Strong transcription	Fetal Muscle Trunk	muscle
17	chr16:75687600-75692400	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr16:75687600-75692400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr16:75687600-75692400	Strong transcription	HepG2	liver
20	chr16:75687600-75693600	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr16:75687600-75694200	Strong transcription	Fetal Muscle Leg	muscle
22	chr16:75687600-75694600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr16:75687600-75695600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr16:75687600-75696000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr16:75687600-75696000	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr16:75687600-75696400	Strong transcription	Primary B cells from cord blood	blood
27	chr16:75687600-75696400	Strong transcription	Fetal Stomach	stomach
28	chr16:75687800-75691400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr16:75687800-75692200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr16:75687800-75692600	Strong transcription	Ovary	ovary
31	chr16:75687800-75693000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr16:75687800-75693000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr16:75687800-75693400	Strong transcription	Left Ventricle	heart
34	chr16:75687800-75694200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr16:75687800-75694600	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr16:75687800-75694800	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr16:75687800-75695400	Strong transcription	Fetal Thymus	thymus
38	chr16:75687800-75695800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr16:75687800-75696200	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr16:75687800-75696200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr16:75688000-75690000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr16:75688000-75692400	Strong transcription	NHEK	skin
43	chr16:75688000-75692800	Strong transcription	Adipose Nuclei	Adipose
44	chr16:75688000-75693000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr16:75688000-75693400	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr16:75688000-75693800	Strong transcription	Fetal Intestine Large	intestine
47	chr16:75688000-75694000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr16:75688000-75694200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr16:75688000-75694800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr16:75688000-75695200	Strong transcription	Liver	Liver

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