Variant report

Variant	rs12655220
Chromosome Location	chr5:126362018-126362019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:126332731..126335455-chr5:126360068..126362849,3	K562	blood:
2	chr5:126357130..126358639-chr5:126360520..126362218,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10051184	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10053382	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10057084	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs10060747	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10065302	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10067364	0.82[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs10071669	0.83[TSI][hapmap]
rs1013662	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs1034844	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10491284	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs10491285	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs10900789	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.83[ASN][1000 genomes]
rs11241912	0.82[MEX][hapmap];0.83[TSI][hapmap]
rs11241913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241916	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11949302	0.83[TSI][hapmap]
rs11956061	0.87[CHB][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs11960799	0.82[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs12515192	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12655640	0.82[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs12657369	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs13189409	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108458	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2108459	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2109215	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs2240527	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2240528	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs248040	0.81[CEU][hapmap]
rs248113	0.84[CEU][hapmap]
rs4131248	0.81[TSI][hapmap]
rs4380710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4835921	0.82[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs4836300	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs4836307	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6595746	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6883871	0.82[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs6891436	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6898415	0.82[EUR][1000 genomes]
rs729607	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7449089	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7706333	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7713933	0.83[TSI][hapmap]
rs7716410	0.87[CHB][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs7721948	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7733551	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7736693	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9327425	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9327428	0.82[CEU][hapmap];0.83[TSI][hapmap];0.86[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
rs12655220	C5orf63	cis	Artery Tibial	GTEx
rs12655220	C5orf63	cis	Nerve Tibial	GTEx
rs12655220	MARCH3	cis	cerebellum	SCAN
rs12655220	MARCH3	cis	parietal	SCAN
rs12655220	MARCH3	cis	Muscle Skeletal	GTEx

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

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	chr5:126347800-126362800	Weak transcription	Fetal Muscle Leg	muscle
4	chr5:126347800-126365200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:126349200-126364400	Weak transcription	Primary T cells from cord blood	blood
6	chr5:126350200-126362800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr5:126351800-126363400	Weak transcription	HUVEC	blood vessel
8	chr5:126351800-126365200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:126352000-126364200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:126355600-126363600	Weak transcription	Primary B cells from cord blood	blood
11	chr5:126356000-126362800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr5:126356000-126364400	Weak transcription	GM12878-XiMat	blood
13	chr5:126357800-126362400	Enhancers	K562	blood
14	chr5:126358600-126362800	Weak transcription	Right Ventricle	heart
15	chr5:126360000-126362200	Enhancers	Adipose Nuclei	Adipose
16	chr5:126360000-126362400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:126360000-126364400	Weak transcription	Small Intestine	intestine
18	chr5:126360200-126362400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr5:126360200-126362800	Weak transcription	Psoas Muscle	Psoas
20	chr5:126360200-126363000	Weak transcription	Left Ventricle	heart
21	chr5:126360200-126364200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr5:126360200-126364400	Weak transcription	Right Atrium	heart
23	chr5:126360200-126364400	Weak transcription	NH-A	brain
24	chr5:126360200-126364600	Weak transcription	Spleen	Spleen
25	chr5:126360400-126362200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:126360400-126364400	Weak transcription	Brain Substantia Nigra	brain
27	chr5:126360800-126362600	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr5:126361000-126364400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:126361000-126364400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:126361200-126362200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr5:126361200-126362200	Enhancers	HSMMtube	muscle
32	chr5:126361200-126362400	Enhancers	Osteobl	bone
33	chr5:126361200-126363000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:126361200-126364400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr5:126361400-126362800	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr5:126361400-126362800	Enhancers	Brain Anterior Caudate	brain
37	chr5:126361400-126363400	Enhancers	Fetal Heart	heart
38	chr5:126361400-126364400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:126361600-126362200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr5:126361600-126362600	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr5:126361600-126363000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr5:126361600-126364400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr5:126361800-126362200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr5:126361800-126362200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr5:126361800-126363400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr5:126361800-126364200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:126361800-126364200	Enhancers	HepG2	liver
48	chr5:126361800-126364400	Weak transcription	Brain Hippocampus Middle	brain
49	chr5:126361800-126365000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr5:126362000-126362800	Enhancers	Fetal Kidney	kidney

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