Variant report

Variant	rs11949302
Chromosome Location	chr5:126282246-126282247
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	chr5:126248689..126250202-chr5:126280275..126282842,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10053382	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs10057084	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10060747	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs10065302	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs10067364	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10071669	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1013662	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1034844	0.96[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs10463826	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10491284	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10900789	1.00[CEU][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs11241912	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11241913	0.83[TSI][hapmap]
rs11956061	1.00[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs11960799	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12515192	0.96[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs12655220	0.83[TSI][hapmap]
rs12655640	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12657369	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2041318	0.81[CEU][hapmap];0.86[CHB][hapmap];0.80[TSI][hapmap]
rs2191209	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs2240527	0.96[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs2240528	0.96[CEU][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs248040	0.86[CHB][hapmap]
rs4131248	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4380710	0.85[TSI][hapmap]
rs4835921	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4836300	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs4836306	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4836307	0.96[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs6860726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6864861	0.85[EUR][1000 genomes]
rs6883871	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6891329	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6891436	0.96[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs6897653	0.82[EUR][1000 genomes]
rs727038	0.81[CEU][hapmap];0.90[CHB][hapmap]
rs729607	0.96[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs7449089	0.86[EUR][1000 genomes]
rs7706333	0.96[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs7713933	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7716410	1.00[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs7721948	0.85[EUR][1000 genomes]
rs7731621	0.85[CEU][hapmap];0.95[CHB][hapmap]
rs7731664	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7733551	0.96[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs7736693	0.96[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs9327424	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9327425	0.85[EUR][1000 genomes]
rs9327426	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9327428	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11949302	C5orf63	cis	Nerve Tibial	GTEx
rs11949302	MARCH3	cis	Muscle Skeletal	GTEx
rs11949302	MARCH3	cis	parietal	SCAN
rs11949302	MARCH3	cis	cerebellum	SCAN
rs11949302	C5orf63	cis	Artery Aorta	GTEx
rs11949302	C5orf63	cis	Esophagus Muscularis	GTEx
rs11949302	C5orf63	cis	Artery Tibial	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126253600-126300400	Weak transcription	Primary B cells from cord blood	blood
2	chr5:126264600-126283000	Weak transcription	Primary T cells from cord blood	blood
3	chr5:126267200-126282600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:126272400-126285200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr5:126272800-126282400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr5:126273000-126283400	Weak transcription	Pancreas	Pancrea
7	chr5:126273000-126285200	Weak transcription	Fetal Muscle Leg	muscle
8	chr5:126275000-126282600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:126275000-126282600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:126275000-126299600	Weak transcription	HSMM	muscle
11	chr5:126275800-126286000	Weak transcription	HSMMtube	muscle
12	chr5:126276200-126290400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:126277600-126282800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:126277800-126282400	Weak transcription	Left Ventricle	heart
15	chr5:126277800-126282800	Weak transcription	Brain Anterior Caudate	brain
16	chr5:126278800-126287000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr5:126279000-126283000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr5:126279000-126283200	Weak transcription	Psoas Muscle	Psoas
19	chr5:126279000-126283200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr5:126279800-126287800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr5:126280600-126286200	Enhancers	Right Ventricle	heart
22	chr5:126281000-126284200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:126281200-126282800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr5:126281400-126283400	Weak transcription	Right Atrium	heart
25	chr5:126281600-126282400	Genic enhancers	K562	blood
26	chr5:126282000-126287000	Enhancers	Fetal Heart	heart
27	chr5:126282200-126282600	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr5:126282200-126282800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:126282200-126283600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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