Variant report

Variant	rs1561330
Chromosome Location	chr2:86206482-86206483
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86203874..86206783-chr2:86210443..86213436,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10173155	0.96[CEU][hapmap];0.84[MEX][hapmap]
rs10181916	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10183118	0.81[ASN][1000 genomes]
rs10186005	0.80[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10189191	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10198260	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1020095	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11890514	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11891625	0.85[ASW][hapmap];0.81[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12470643	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12472588	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12476390	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12714162	0.85[ASN][1000 genomes]
rs12714163	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12714164	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12714165	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13000793	0.85[ASW][hapmap];0.81[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1438153	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1438155	0.88[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1866242	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1866245	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2083168	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2099616	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2099617	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2118521	0.80[AFR][1000 genomes]
rs3937593	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4346389	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4480982	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4514874	0.81[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4832018	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4832019	0.81[ASN][1000 genomes]
rs4832020	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4832232	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4832233	0.96[CEU][hapmap];0.84[MEX][hapmap]
rs6547651	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6547653	0.81[AMR][1000 genomes]
rs6547654	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6706720	0.93[ASN][1000 genomes]
rs6708525	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6724025	0.80[AFR][1000 genomes]
rs6737454	0.81[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7586985	0.81[AMR][1000 genomes]
rs7595420	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7597264	0.88[ASN][1000 genomes]
rs7599326	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7606897	0.83[AMR][1000 genomes]
rs7607138	0.81[AMR][1000 genomes]
rs893442	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs934829	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs934830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs934831	0.81[AMR][1000 genomes];0.80[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	nsv1001104	chr2:86182021-86271923	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv535807	chr2:86182021-86271923	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1561330	ST3GAL5	cis	cerebellum	SCAN
rs1561330	IMMT	Cis_1M	lymphoblastoid	RTeQTL
rs1561330	MRPL35	cis	parietal	SCAN
rs1561330	MRPL35	cis	normal skin	skin_eQTL
rs1561330	IMMT	cis	cerebellum	SCAN
rs1561330	REEP1	cis	parietal	SCAN
rs1561330	IMMT	cis	lymphoblastoid	seeQTL
rs1561330	IMMT	cis	uninvolved skin	skin_eQTL
rs1561330	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs1561330	MRPL35	cis	cerebellum	SCAN
rs1561330	C2orf51	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86203800-86206600	Weak transcription	Right Ventricle	heart
2	chr2:86204000-86206600	Weak transcription	Lung	lung
3	chr2:86204000-86208800	Weak transcription	Gastric	stomach
4	chr2:86204000-86221000	Weak transcription	Right Atrium	heart
5	chr2:86204400-86206600	Enhancers	Fetal Heart	heart
6	chr2:86205400-86206600	Enhancers	A549	lung
7	chr2:86205400-86207000	Enhancers	Liver	Liver
8	chr2:86205400-86207000	Enhancers	Hela-S3	cervix
9	chr2:86205400-86208000	Enhancers	Stomach Mucosa	stomach
10	chr2:86205600-86206800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:86205600-86206800	Enhancers	Colon Smooth Muscle	Colon
12	chr2:86205600-86207000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:86205600-86207000	Enhancers	Adipose Nuclei	Adipose
14	chr2:86205600-86208600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:86205800-86206800	Enhancers	Primary B cells from cord blood	blood
16	chr2:86205800-86206800	Enhancers	Brain Germinal Matrix	brain
17	chr2:86205800-86206800	Weak transcription	Fetal Muscle Leg	muscle
18	chr2:86205800-86207000	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr2:86205800-86207200	Enhancers	NHDF-Ad	bronchial
20	chr2:86205800-86208800	Weak transcription	Spleen	Spleen
21	chr2:86205800-86214200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:86206000-86206600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:86206000-86206800	Weak transcription	Psoas Muscle	Psoas
24	chr2:86206000-86206800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:86206000-86207000	Enhancers	Primary B cells from peripheral blood	blood
26	chr2:86206000-86207000	Weak transcription	Brain Hippocampus Middle	brain
27	chr2:86206000-86207000	Enhancers	Osteobl	bone
28	chr2:86206000-86207600	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr2:86206000-86207600	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr2:86206200-86206800	Weak transcription	Left Ventricle	heart
31	chr2:86206200-86207000	Enhancers	GM12878-XiMat	blood
32	chr2:86206200-86207800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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