Variant report

Variant	rs7716410
Chromosome Location	chr5:126214489-126214490
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	chr5:126212812-126215063	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:126214300..126217268-chr5:126520961..126522578,2	K562	blood:
2	chr5:126213898..126216228-chr5:126364824..126367570,2	K562	blood:

Variant related genes	Relation type
MARCH3	TF binding region
ENSG00000173926	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10053382	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs10057084	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs10060747	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs10065302	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs10067364	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs10071669	1.00[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs1013662	0.96[CEU][hapmap]
rs1034844	0.82[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10491284	0.96[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs10900789	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11241912	1.00[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs11241913	0.87[CHB][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs11949302	1.00[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs11956061	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11960799	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs12515192	0.88[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs12655220	0.87[CHB][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs12655640	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs12657369	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs2240527	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs2240528	0.82[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes]
rs28528146	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4131248	1.00[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs4380710	0.87[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs4835921	0.96[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs4836300	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4836306	0.80[EUR][1000 genomes]
rs4836307	0.88[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6860726	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6864861	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6883871	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs6891329	0.84[EUR][1000 genomes]
rs6891436	0.94[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.82[EUR][1000 genomes]
rs6897653	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs729607	0.88[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes]
rs7449089	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7706333	0.88[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs7713933	0.93[CEU][hapmap];0.93[TSI][hapmap]
rs7721948	0.84[EUR][1000 genomes]
rs7733551	0.94[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7736693	0.88[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs9327425	0.84[EUR][1000 genomes]
rs9327428	0.96[CEU][hapmap];0.93[TSI][hapmap]

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	nsv949054	chr5:125918148-126254480	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv534292	chr5:125993451-126259315	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers 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	36 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7716410	C5orf63	cis	Nerve Tibial	GTEx
rs7716410	MARCH3	cis	parietal	SCAN
rs7716410	C5orf63	cis	Artery Tibial	GTEx
rs7716410	MARCH3	cis	cerebellum	SCAN
rs7716410	C5orf63	cis	Artery Aorta	GTEx
rs7716410	MARCH3	cis	Muscle Skeletal	GTEx
rs7716410	C5orf63	cis	Esophagus Muscularis	GTEx
rs7716410	MEGF10	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126201800-126253400	Weak transcription	A549	lung
2	chr5:126205200-126216200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr5:126205200-126219200	Weak transcription	Osteobl	bone
4	chr5:126205200-126245600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr5:126205400-126215000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr5:126205400-126217200	Weak transcription	Brain Anterior Caudate	brain
7	chr5:126205400-126219200	Weak transcription	Brain Substantia Nigra	brain
8	chr5:126205400-126219600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:126205400-126220200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:126205400-126220800	Weak transcription	Thymus	Thymus
11	chr5:126205400-126221400	Weak transcription	Fetal Thymus	thymus
12	chr5:126205400-126245600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr5:126205600-126215400	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr5:126205600-126220200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:126205600-126223400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr5:126205600-126238200	Weak transcription	Primary T cells from cord blood	blood
17	chr5:126206400-126220400	Weak transcription	Lung	lung
18	chr5:126206800-126214600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr5:126206800-126220000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:126207600-126221600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr5:126208000-126214600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr5:126209000-126219600	Weak transcription	HSMMtube	muscle
23	chr5:126210400-126215000	Enhancers	Fetal Heart	heart
24	chr5:126210600-126214600	Strong transcription	Primary B cells from peripheral blood	blood
25	chr5:126210600-126223400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr5:126211200-126219600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:126211200-126221800	Weak transcription	Fetal Intestine Small	intestine
28	chr5:126211200-126231600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:126211600-126214800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr5:126211600-126218400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr5:126211600-126220200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:126211800-126223400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr5:126212000-126236800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:126212800-126214600	Enhancers	Ovary	ovary
35	chr5:126213000-126215800	Strong transcription	K562	blood
36	chr5:126213400-126214600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:126213600-126219200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:126213800-126214600	Enhancers	Right Atrium	heart
39	chr5:126213800-126215000	Weak transcription	Placenta	Placenta
40	chr5:126213800-126215000	Enhancers	Right Ventricle	heart
41	chr5:126213800-126219200	Weak transcription	HUVEC	blood vessel
42	chr5:126214000-126215000	Enhancers	Adipose Nuclei	Adipose
43	chr5:126214000-126219400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:126214200-126214600	Enhancers	Fetal Kidney	kidney
45	chr5:126214200-126214600	Enhancers	Left Ventricle	heart
46	chr5:126214200-126214800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr5:126214200-126215000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr5:126214200-126219200	Weak transcription	HSMM	muscle
49	chr5:126214200-126237400	Weak transcription	Fetal Brain Female	brain
50	chr5:126214200-126238600	Weak transcription	Fetal Muscle Leg	muscle

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