Variant report

Variant	rs17470919
Chromosome Location	chr4:48144525-48144526
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:48143682-48144579	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:48144010-48144530	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48141748..48144032-chr4:48144132..48146805,2	K562	blood:

Variant related genes	Relation type
TEC	TF binding region
ENSG00000135605	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10016563	0.87[CEU][hapmap];0.91[EUR][1000 genomes]
rs10021919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10033663	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1159075	0.87[JPT][hapmap]
rs11942525	0.93[JPT][hapmap]
rs16861044	0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs16861106	0.93[JPT][hapmap]
rs16861108	0.93[JPT][hapmap]
rs17470892	0.80[EUR][1000 genomes]
rs17471024	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17471142	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs17574371	0.80[EUR][1000 genomes]
rs17574399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2456928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2661532	0.93[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2661535	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28408546	0.87[ASN][1000 genomes]
rs28521484	0.80[EUR][1000 genomes]
rs28538414	0.87[ASN][1000 genomes]
rs28702422	0.94[EUR][1000 genomes]
rs3749503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792619	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs55683170	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55809586	0.91[EUR][1000 genomes]
rs6814046	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6814614	0.87[EUR][1000 genomes]
rs6819804	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6829390	0.81[JPT][hapmap]
rs73244489	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7654182	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7682890	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7684558	0.90[EUR][1000 genomes]
rs955692	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs996222	0.80[EUR][1000 genomes]
rs996223	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9991974	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17470919	TEC	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48129800-48157400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:48130400-48152200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:48130400-48155400	Weak transcription	Psoas Muscle	Psoas
4	chr4:48130400-48156200	Weak transcription	Adipose Nuclei	Adipose
5	chr4:48130400-48156800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:48130400-48157600	Weak transcription	Colonic Mucosa	Colon
7	chr4:48130600-48146000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr4:48132000-48157000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:48132000-48157200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:48133000-48151400	Weak transcription	HSMMtube	muscle
11	chr4:48133000-48153000	Weak transcription	Placenta	Placenta
12	chr4:48137800-48153600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:48138400-48157400	Weak transcription	Aorta	Aorta
14	chr4:48138600-48150400	Weak transcription	Fetal Lung	lung
15	chr4:48138600-48155800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr4:48138800-48147000	Weak transcription	Esophagus	oesophagus
17	chr4:48139200-48154600	Weak transcription	Fetal Intestine Small	intestine
18	chr4:48139200-48155600	Weak transcription	Fetal Intestine Large	intestine
19	chr4:48139200-48157600	Weak transcription	Gastric	stomach
20	chr4:48139200-48159000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr4:48139800-48147000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:48139800-48155400	Weak transcription	Spleen	Spleen
23	chr4:48139800-48155800	Weak transcription	Lung	lung
24	chr4:48140200-48146800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr4:48140200-48157400	Weak transcription	Pancreas	Pancrea
26	chr4:48141000-48152200	Weak transcription	Left Ventricle	heart
27	chr4:48141000-48155800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr4:48141200-48145000	Weak transcription	K562	blood
29	chr4:48141200-48146600	Weak transcription	Liver	Liver
30	chr4:48141200-48151600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr4:48141200-48155400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr4:48141400-48144600	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr4:48141800-48155600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr4:48142000-48145000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr4:48142400-48155600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:48142600-48155400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr4:48142800-48144800	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr4:48142800-48152200	Strong transcription	GM12878-XiMat	blood
39	chr4:48143000-48145600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr4:48143000-48147000	Weak transcription	Primary B cells from cord blood	blood
41	chr4:48143000-48148800	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr4:48143000-48152200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:48143000-48155800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr4:48143000-48157600	Weak transcription	Fetal Thymus	thymus
45	chr4:48143000-48157600	Weak transcription	Thymus	Thymus
46	chr4:48143200-48155600	Weak transcription	Primary T cells from cord blood	blood
47	chr4:48144000-48145600	Strong transcription	Primary hematopoietic stem cells	blood
48	chr4:48144000-48155400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr4:48144400-48151800	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr4:48144400-48155800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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