Variant report

Variant	rs2704426
Chromosome Location	chr4:48150543-48150544
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48148512..48152752-chr4:48153089..48156542,4	K562	blood:
2	chr4:48148666..48151468-chr4:48270937..48272874,2	K562	blood:
3	chr4:48148814..48151468-chr4:48270751..48272874,2	K562	blood:

Variant related genes	Relation type
ENSG00000135605	Chromatin interaction
ENSG00000202014	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10027991	1.00[ASN][1000 genomes]
rs10805164	1.00[JPT][hapmap]
rs10805165	1.00[JPT][hapmap]
rs10938524	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11730441	0.85[JPT][hapmap]
rs11944549	1.00[ASN][1000 genomes]
rs11945978	1.00[JPT][hapmap]
rs12332001	1.00[ASN][1000 genomes]
rs12499541	1.00[JPT][hapmap]
rs12512766	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13104849	1.00[JPT][hapmap]
rs1466994	1.00[JPT][hapmap]
rs1507919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860999	0.95[ASN][1000 genomes]
rs1961975	1.00[JPT][hapmap]
rs2089509	1.00[JPT][hapmap]
rs2089510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2089511	1.00[JPT][hapmap]
rs2243840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271173	1.00[JPT][hapmap]
rs2464502	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2661529	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2661543	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2661544	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2661547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2661548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704399	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2704433	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2704435	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2704436	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792620	1.00[JPT][hapmap]
rs3792621	1.00[JPT][hapmap]
rs3792622	1.00[JPT][hapmap]
rs3805179	1.00[JPT][hapmap]
rs3805184	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4695340	1.00[JPT][hapmap]
rs4695341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4695344	1.00[JPT][hapmap]
rs6447616	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814443	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6819592	0.97[ASN][1000 genomes]
rs6845941	1.00[JPT][hapmap]
rs7659164	1.00[ASN][1000 genomes]
rs7678246	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7689953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs882715	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[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
rs2704426	TXK	cis	multi-tissue	Pritchard

Chromatin state (count:49 , 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	chr4:48132000-48157000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:48132000-48157200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:48133000-48151400	Weak transcription	HSMMtube	muscle
10	chr4:48133000-48153000	Weak transcription	Placenta	Placenta
11	chr4:48137800-48153600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:48138400-48157400	Weak transcription	Aorta	Aorta
13	chr4:48138600-48155800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr4:48139200-48154600	Weak transcription	Fetal Intestine Small	intestine
15	chr4:48139200-48155600	Weak transcription	Fetal Intestine Large	intestine
16	chr4:48139200-48157600	Weak transcription	Gastric	stomach
17	chr4:48139200-48159000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr4:48139800-48155400	Weak transcription	Spleen	Spleen
19	chr4:48139800-48155800	Weak transcription	Lung	lung
20	chr4:48140200-48157400	Weak transcription	Pancreas	Pancrea
21	chr4:48141000-48152200	Weak transcription	Left Ventricle	heart
22	chr4:48141000-48155800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:48141200-48151600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr4:48141200-48155400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr4:48141800-48155600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:48142400-48155600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:48142600-48155400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr4:48142800-48152200	Strong transcription	GM12878-XiMat	blood
29	chr4:48143000-48152200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:48143000-48155800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr4:48143000-48157600	Weak transcription	Fetal Thymus	thymus
32	chr4:48143000-48157600	Weak transcription	Thymus	Thymus
33	chr4:48143200-48155600	Weak transcription	Primary T cells from cord blood	blood
34	chr4:48144000-48155400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr4:48144400-48151800	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr4:48144400-48155800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:48144600-48151600	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr4:48144800-48157200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr4:48145800-48151400	Weak transcription	K562	blood
40	chr4:48146600-48156000	Strong transcription	Primary hematopoietic stem cells	blood
41	chr4:48147600-48155600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:48147600-48155600	Weak transcription	Esophagus	oesophagus
43	chr4:48147800-48153000	Weak transcription	Primary B cells from peripheral blood	blood
44	chr4:48147800-48155600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr4:48148000-48155600	Weak transcription	Primary B cells from cord blood	blood
46	chr4:48150000-48164000	Weak transcription	Hela-S3	cervix
47	chr4:48150200-48151400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr4:48150400-48151200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:48150400-48152600	Strong transcription	Liver	Liver

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