Variant report

Variant	rs12655640
Chromosome Location	chr5:126329208-126329209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:126328847..126331239-chr5:126388001..126390395,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10053382	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10057084	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10060747	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10065302	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10067364	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10071669	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1013662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1034844	1.00[CEU][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10463826	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10491284	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10900789	0.96[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs11241912	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs11241913	0.82[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs11949302	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]
rs11956061	0.96[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs11960799	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[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];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12515192	1.00[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs12655220	0.82[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs12657369	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13154281	0.87[EUR][1000 genomes]
rs13189409	0.91[EUR][1000 genomes]
rs2041318	0.85[CEU][hapmap];0.86[CHB][hapmap];0.80[TSI][hapmap]
rs2108458	0.91[EUR][1000 genomes]
rs2108459	0.91[EUR][1000 genomes]
rs2191209	0.92[CEU][hapmap];0.95[CHB][hapmap];0.80[EUR][1000 genomes]
rs2240527	1.00[CEU][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2240528	1.00[CEU][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs248040	0.86[CHB][hapmap]
rs248081	0.84[CEU][hapmap]
rs248107	0.89[CEU][hapmap]
rs4131248	0.86[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4380710	0.82[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4835921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4835922	0.87[EUR][1000 genomes]
rs4836300	0.85[TSI][hapmap]
rs4836306	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4836307	1.00[CEU][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6860726	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6883871	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6891329	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6891436	1.00[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6899133	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs727038	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs729607	1.00[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7706333	1.00[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs7713933	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7716410	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs7721948	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7729349	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7731621	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs7733551	1.00[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs7736693	1.00[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs9327424	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9327425	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9327426	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9327428	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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
rs12655640	C5orf63	cis	Esophagus Muscularis	GTEx
rs12655640	C5orf63	cis	Artery Aorta	GTEx
rs12655640	C5orf63	cis	Nerve Tibial	GTEx
rs12655640	MARCH3	cis	Muscle Skeletal	GTEx
rs12655640	C5orf63	cis	Artery Tibial	GTEx
rs12655640	MARCH3	cis	cerebellum	SCAN
rs12655640	MARCH3	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126309000-126331000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:126309000-126331600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:126309400-126334000	Weak transcription	Small Intestine	intestine
4	chr5:126312800-126331600	Weak transcription	HSMM	muscle
5	chr5:126320800-126356000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:126323400-126334800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr5:126323600-126330400	Weak transcription	Right Atrium	heart
8	chr5:126323600-126334000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr5:126324000-126330400	Weak transcription	Left Ventricle	heart
10	chr5:126324000-126330800	Weak transcription	Right Ventricle	heart
11	chr5:126324000-126333800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:126325600-126330000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr5:126325600-126333800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:126325600-126333800	Weak transcription	HUVEC	blood vessel
15	chr5:126325600-126342000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr5:126326200-126331600	Enhancers	Primary B cells from peripheral blood	blood
17	chr5:126327800-126335600	Enhancers	Fetal Heart	heart
18	chr5:126328200-126333800	Weak transcription	Primary B cells from cord blood	blood
19	chr5:126328800-126329400	Enhancers	Stomach Mucosa	stomach
20	chr5:126328800-126329600	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr5:126328800-126329800	Enhancers	K562	blood
22	chr5:126328800-126335400	Enhancers	Psoas Muscle	Psoas
23	chr5:126329000-126329400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr5:126329000-126329600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:126329000-126334000	Weak transcription	Gastric	stomach
26	chr5:126329200-126333800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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