Variant report

Variant	rs13189409
Chromosome Location	chr5:126359876-126359877
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:126351866..126355437-chr5:126358417..126361637,3	K562	blood:
2	chr5:126337289..126339518-chr5:126359619..126361646,2	K562	blood:
3	chr5:126111375..126113810-chr5:126357388..126359985,2	K562	blood:
4	chr5:126357040..126360178-chr5:126363426..126367138,4	MCF-7	breast:
5	chr5:126351866..126355719-chr5:126358417..126361637,4	K562	blood:
6	chr5:126317060..126319514-chr5:126359068..126361559,2	K562	blood:

Variant related genes	Relation type
ENSG00000173926	Chromatin interaction
ENSG00000251072	Chromatin interaction
ENSG00000113368	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10051184	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10053382	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10057084	0.87[EUR][1000 genomes]
rs10060747	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10065302	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10067364	0.91[EUR][1000 genomes]
rs1013662	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1034844	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10463826	0.87[EUR][1000 genomes]
rs10491284	0.82[EUR][1000 genomes]
rs10900789	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11241913	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241916	0.83[EUR][1000 genomes]
rs11956061	0.83[EUR][1000 genomes]
rs11960799	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12515192	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12655220	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655640	0.91[EUR][1000 genomes]
rs12657369	0.87[EUR][1000 genomes]
rs13154281	0.85[EUR][1000 genomes]
rs2108458	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2108459	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240527	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2240528	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3915634	0.82[EUR][1000 genomes]
rs4380710	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4835921	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4835922	0.85[EUR][1000 genomes]
rs4836306	0.86[EUR][1000 genomes]
rs4836307	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6595746	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6883871	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6891436	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6899133	0.85[EUR][1000 genomes]
rs729607	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7449089	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7706333	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7721948	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7733551	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7736693	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9327424	0.87[EUR][1000 genomes]
rs9327425	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9327426	0.87[EUR][1000 genomes]
rs9327428	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024265	chr5:126213004-126691163	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv869897	chr5:126224358-126445210	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13189409	MARCH3	cis	Muscle Skeletal	GTEx
rs13189409	C5orf63	cis	Esophagus Muscularis	GTEx
rs13189409	C5orf63	cis	Artery Tibial	GTEx
rs13189409	C5orf63	cis	Nerve Tibial	GTEx
rs13189409	C5orf63	cis	Artery Aorta	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126334400-126363000	Weak transcription	Ovary	ovary
2	chr5:126345600-126362400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr5:126347800-126360000	Weak transcription	Brain Substantia Nigra	brain
4	chr5:126347800-126362800	Weak transcription	Fetal Muscle Leg	muscle
5	chr5:126347800-126365200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:126349200-126364400	Weak transcription	Primary T cells from cord blood	blood
7	chr5:126350200-126362800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr5:126351400-126360600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:126351800-126363400	Weak transcription	HUVEC	blood vessel
10	chr5:126351800-126365200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:126352000-126361200	Weak transcription	HSMM	muscle
12	chr5:126352000-126364200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr5:126355600-126363600	Weak transcription	Primary B cells from cord blood	blood
14	chr5:126355800-126361200	Weak transcription	HSMMtube	muscle
15	chr5:126356000-126362800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr5:126356000-126364400	Weak transcription	GM12878-XiMat	blood
17	chr5:126357800-126362400	Enhancers	K562	blood
18	chr5:126358200-126360000	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr5:126358200-126361400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr5:126358600-126362000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr5:126358600-126362800	Weak transcription	Right Ventricle	heart
22	chr5:126358800-126360000	Weak transcription	Left Ventricle	heart
23	chr5:126359000-126361800	Weak transcription	HepG2	liver
24	chr5:126359600-126360000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:126359600-126360200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr5:126359600-126360200	Enhancers	Psoas Muscle	Psoas
27	chr5:126359600-126360200	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr5:126359600-126360200	Active TSS	Spleen	Spleen
29	chr5:126359800-126360000	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr5:126359800-126360000	Enhancers	Small Intestine	intestine
31	chr5:126359800-126360400	Enhancers	Fetal Heart	heart

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