Variant report

Variant	rs57549677
Chromosome Location	chr5:74025150-74025151
allele	A/G
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	chr5:74024645-74025213	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74018853..74021864-chr5:74023433..74025995,4	K562	blood:
2	chr5:74022416..74025189-chr5:74034895..74036734,2	K562	blood:

Variant related genes	Relation type
RNU6-658P	TF binding region
ENSG00000207336	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1048167	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10515192	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515194	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515199	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11739122	0.81[AFR][1000 genomes]
rs11742773	0.85[AFR][1000 genomes]
rs11959570	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1350097	0.82[AFR][1000 genomes]
rs16872220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872231	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872235	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872242	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872259	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872323	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872345	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872349	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872362	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17561738	0.86[ASN][1000 genomes]
rs2084116	0.85[AFR][1000 genomes]
rs2084118	0.85[AFR][1000 genomes]
rs2100033	0.85[AFR][1000 genomes]
rs3733794	0.83[AFR][1000 genomes]
rs55899032	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55920995	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56127814	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56192858	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56203772	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57202395	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58864890	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60492282	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60663580	0.86[AFR][1000 genomes]
rs62366414	0.86[AFR][1000 genomes]
rs6453076	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453079	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453082	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6861935	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6870806	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6873912	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873998	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6877188	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881400	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6882035	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6882499	0.80[AFR][1000 genomes]
rs6883061	0.85[AFR][1000 genomes]
rs6883278	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6883420	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6884338	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6885675	0.85[AFR][1000 genomes]
rs6894177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898684	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764630	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764647	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764648	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764650	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764654	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764655	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764656	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764657	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764663	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764669	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764675	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764676	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764683	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764684	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764687	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764690	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72766504	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7705519	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7713812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7732440	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7732843	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957680	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9686657	0.85[AFR][1000 genomes]
rs9765469	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598653	chr5:73992881-74095542	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers 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	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs57549677	NSA2	cis	Muscle Skeletal	GTEx
rs57549677	NSA2	cis	Skin Sun Exposed Lower leg	GTEx
rs57549677	NSA2	cis	Heart Left Ventricle	GTEx
rs57549677	NSA2	cis	Esophagus Muscularis	GTEx
rs57549677	NSA2	cis	Thyroid	GTEx
rs57549677	NSA2	cis	Adipose Subcutaneous	GTEx
rs57549677	TINP1	cis	multi-tissue	Pritchard
rs57549677	NSA2	cis	Whole Blood	GTEx
rs57549677	NSA2	cis	Stomach	GTEx
rs57549677	NSA2	cis	lung	GTEx
rs57549677	NSA2	cis	Artery Aorta	GTEx
rs57549677	TINP1	Cis_1M	lymphoblastoid	RTeQTL
rs57549677	NSA2	cis	Esophagus Mucosa	GTEx
rs57549677	NSA2	cis	Artery Tibial	GTEx
rs57549677	NSA2	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:73982000-74061800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:73983000-74027000	Weak transcription	Fetal Heart	heart
3	chr5:73983200-74030200	Weak transcription	Small Intestine	intestine
4	chr5:73999800-74060800	Weak transcription	Pancreas	Pancrea
5	chr5:73999800-74062200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:74002600-74030800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:74002600-74031800	Weak transcription	Esophagus	oesophagus
8	chr5:74002600-74041200	Weak transcription	Colonic Mucosa	Colon
9	chr5:74002600-74051600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:74002600-74061800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:74008400-74028800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:74008400-74036200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:74008400-74047800	Strong transcription	Placenta	Placenta
14	chr5:74008400-74060200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr5:74008400-74060200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr5:74008600-74044200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:74008800-74035200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr5:74008800-74036000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr5:74010000-74036200	Strong transcription	Liver	Liver
20	chr5:74010200-74036000	Strong transcription	Duodenum Mucosa	Duodenum
21	chr5:74010200-74038200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr5:74010200-74048000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr5:74010400-74036400	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr5:74010400-74059600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr5:74011200-74044200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr5:74011400-74036800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:74012000-74051600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:74012200-74050400	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr5:74012600-74027400	Strong transcription	Left Ventricle	heart
30	chr5:74012600-74027600	Strong transcription	Dnd41	blood
31	chr5:74012600-74034800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr5:74012800-74036200	Strong transcription	Fetal Intestine Large	intestine
33	chr5:74013000-74027800	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr5:74013400-74027200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:74013400-74047400	Strong transcription	Adipose Nuclei	Adipose
36	chr5:74013600-74028800	Strong transcription	HSMM	muscle
37	chr5:74014400-74047800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr5:74014400-74051600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:74015200-74048600	Weak transcription	Stomach Mucosa	stomach
40	chr5:74016000-74027400	Strong transcription	Fetal Muscle Leg	muscle
41	chr5:74016400-74052400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr5:74016600-74026400	Weak transcription	Lung	lung
43	chr5:74016600-74026800	Weak transcription	Fetal Intestine Small	intestine
44	chr5:74018000-74039600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr5:74018000-74060800	Weak transcription	Gastric	stomach
46	chr5:74018200-74027000	Weak transcription	NHEK	skin
47	chr5:74018200-74030600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr5:74018200-74036200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:74018600-74025800	Weak transcription	Brain Germinal Matrix	brain
50	chr5:74018600-74062000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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