Variant report

Variant	rs17471024
Chromosome Location	chr4:48163461-48163462
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10016563	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021919	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10033663	0.87[EUR][1000 genomes]
rs12331972	1.00[ASN][1000 genomes]
rs17470892	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17470919	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17574371	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17574399	1.00[CEU][hapmap];0.90[GIH][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2456928	1.00[CEU][hapmap];0.90[GIH][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs2661535	0.95[EUR][1000 genomes]
rs28521484	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28702422	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28740900	1.00[ASN][1000 genomes]
rs3749503	1.00[CEU][hapmap];0.90[GIH][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs55683170	0.87[EUR][1000 genomes]
rs55809586	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814046	0.93[EUR][1000 genomes]
rs6814614	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6819804	0.87[EUR][1000 genomes]
rs6837324	0.83[ASW][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs6845196	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73244489	0.93[EUR][1000 genomes]
rs7654182	0.95[EUR][1000 genomes]
rs7654466	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7682890	0.95[EUR][1000 genomes]
rs7684558	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs955692	0.87[EUR][1000 genomes]
rs996222	1.00[CHB][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs996223	1.00[CEU][hapmap];0.90[GIH][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs9991974	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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17471024	FRYL	cis	cerebellum	SCAN
rs17471024	TEC	cis	parietal	SCAN
rs17471024	TXK	cis	parietal	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	chr4:48152600-48164000	Weak transcription	HSMM	muscle
3	chr4:48156000-48168000	Weak transcription	Esophagus	oesophagus
4	chr4:48157800-48175400	Weak transcription	Colon Smooth Muscle	Colon
5	chr4:48157800-48181000	Weak transcription	Pancreas	Pancrea
6	chr4:48158400-48164000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:48158400-48164000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:48158400-48168000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr4:48158400-48168000	Weak transcription	Gastric	stomach
10	chr4:48158400-48169600	Weak transcription	K562	blood
11	chr4:48158400-48170800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:48158400-48171400	Weak transcription	Fetal Lung	lung
13	chr4:48158400-48171400	Weak transcription	Left Ventricle	heart
14	chr4:48158400-48171400	Weak transcription	Psoas Muscle	Psoas
15	chr4:48158400-48172200	Weak transcription	Colonic Mucosa	Colon
16	chr4:48158400-48172200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:48158400-48175000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:48158400-48175600	Weak transcription	Adipose Nuclei	Adipose
19	chr4:48158400-48180600	Weak transcription	Spleen	Spleen
20	chr4:48158400-48181800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:48158400-48190000	Weak transcription	Aorta	Aorta
22	chr4:48158600-48164200	Weak transcription	Liver	Liver
23	chr4:48158600-48167600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr4:48158600-48179200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr4:48158600-48179400	Weak transcription	Fetal Intestine Small	intestine
26	chr4:48158800-48164200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr4:48158800-48167800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:48158800-48168000	Weak transcription	Fetal Intestine Large	intestine
29	chr4:48158800-48168800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr4:48158800-48171000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr4:48158800-48174600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:48158800-48175600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr4:48158800-48180200	Weak transcription	Fetal Thymus	thymus
34	chr4:48159400-48177200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr4:48159600-48166000	Strong transcription	Primary hematopoietic stem cells	blood
36	chr4:48159600-48167600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr4:48159600-48169800	Strong transcription	GM12878-XiMat	blood
38	chr4:48159800-48169600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr4:48160000-48164600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr4:48160400-48168000	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr4:48160400-48168800	Weak transcription	Primary B cells from cord blood	blood
42	chr4:48160400-48174400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr4:48161200-48164200	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr4:48163200-48164200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr4:48163200-48164800	Enhancers	HSMMtube	muscle

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