Variant report

Variant	rs12502528
Chromosome Location	chr4:48159351-48159352
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	chr4:48159219..48161571-chr4:48166028..48167531,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1008277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10805164	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs10805165	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs10938522	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11730441	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11733531	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11941829	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11945978	0.92[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs12502268	0.91[EUR][1000 genomes]
rs12512837	0.92[EUR][1000 genomes]
rs12649067	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13104849	1.00[CEU][hapmap];0.93[GIH][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs13146998	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1466990	0.92[EUR][1000 genomes]
rs1466991	0.92[EUR][1000 genomes]
rs1466992	0.92[EUR][1000 genomes]
rs1466993	0.92[EUR][1000 genomes]
rs1466994	0.92[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs1466995	0.92[EUR][1000 genomes]
rs1466996	0.92[EUR][1000 genomes]
rs1961974	0.92[EUR][1000 genomes]
rs1961975	0.92[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2071027	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2089509	0.92[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2089511	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs2256425	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271173	0.89[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2271174	0.92[EUR][1000 genomes]
rs34990592	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3792620	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs3792621	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs3792622	1.00[CEU][hapmap];0.93[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs3805179	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs3913948	0.95[EUR][1000 genomes]
rs4323077	0.92[EUR][1000 genomes]
rs4392481	0.92[EUR][1000 genomes]
rs4392482	0.92[EUR][1000 genomes]
rs4504220	0.90[EUR][1000 genomes]
rs4695338	0.91[YRI][hapmap]
rs4695339	0.92[EUR][1000 genomes]
rs4695340	0.92[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs4695342	0.92[EUR][1000 genomes]
rs4695343	0.92[EUR][1000 genomes]
rs4695344	0.92[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs4695346	0.92[EUR][1000 genomes]
rs4695347	0.92[EUR][1000 genomes]
rs4695348	0.92[EUR][1000 genomes]
rs4695349	0.92[EUR][1000 genomes]
rs4695350	0.92[EUR][1000 genomes]
rs61326763	0.89[EUR][1000 genomes]
rs62309327	0.92[EUR][1000 genomes]
rs6844543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6845941	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6851861	0.91[EUR][1000 genomes]
rs6858716	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7654108	0.92[EUR][1000 genomes]
rs7668350	0.91[EUR][1000 genomes]
rs7669393	0.92[EUR][1000 genomes]
rs7670351	0.92[EUR][1000 genomes]
rs7671720	0.89[EUR][1000 genomes]
rs7680519	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7695902	0.92[EUR][1000 genomes]
rs7696119	0.92[EUR][1000 genomes]
rs7696271	0.92[EUR][1000 genomes]
rs885443	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs955691	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482316	chr4:48151953-48338746	Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12502528	NFXL1	cis	multi-tissue	Pritchard
rs12502528	FRYL	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48150000-48164000	Weak transcription	Hela-S3	cervix
2	chr4:48152600-48163200	Weak transcription	HSMMtube	muscle
3	chr4:48152600-48164000	Weak transcription	HSMM	muscle
4	chr4:48153000-48160400	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr4:48155200-48159400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:48155400-48159600	ZNF genes & repeats	GM12878-XiMat	blood
7	chr4:48155400-48160000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:48155800-48159400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:48156000-48159600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
10	chr4:48156000-48168000	Weak transcription	Esophagus	oesophagus
11	chr4:48157800-48175400	Weak transcription	Colon Smooth Muscle	Colon
12	chr4:48157800-48181000	Weak transcription	Pancreas	Pancrea
13	chr4:48158400-48159800	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:48158400-48162200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:48158400-48164000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:48158400-48164000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:48158400-48168000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr4:48158400-48168000	Weak transcription	Gastric	stomach
19	chr4:48158400-48169600	Weak transcription	K562	blood
20	chr4:48158400-48170800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:48158400-48171400	Weak transcription	Fetal Lung	lung
22	chr4:48158400-48171400	Weak transcription	Left Ventricle	heart
23	chr4:48158400-48171400	Weak transcription	Psoas Muscle	Psoas
24	chr4:48158400-48172200	Weak transcription	Colonic Mucosa	Colon
25	chr4:48158400-48172200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:48158400-48175000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr4:48158400-48175600	Weak transcription	Adipose Nuclei	Adipose
28	chr4:48158400-48180600	Weak transcription	Spleen	Spleen
29	chr4:48158400-48181800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:48158400-48190000	Weak transcription	Aorta	Aorta
31	chr4:48158600-48159800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:48158600-48161200	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr4:48158600-48164200	Weak transcription	Liver	Liver
34	chr4:48158600-48167600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr4:48158600-48179200	Weak transcription	Duodenum Mucosa	Duodenum
36	chr4:48158600-48179400	Weak transcription	Fetal Intestine Small	intestine
37	chr4:48158800-48159600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr4:48158800-48164200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr4:48158800-48167800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr4:48158800-48168000	Weak transcription	Fetal Intestine Large	intestine
41	chr4:48158800-48168800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr4:48158800-48171000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr4:48158800-48174600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr4:48158800-48175600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:48158800-48180200	Weak transcription	Fetal Thymus	thymus

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