Variant report

Variant	rs58479554
Chromosome Location	chr15:57404406-57404407
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	chr15:57403095..57404934-chr15:57406973..57408733,2	K562	blood:
2	chr15:57397844..57400555-chr15:57402758..57405029,3	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10467927	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10467928	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10467929	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11071308	0.83[EUR][1000 genomes]
rs11856411	0.80[EUR][1000 genomes]
rs12101455	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591430	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13379847	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16977222	0.80[EUR][1000 genomes]
rs16977243	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16977270	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1841697	0.85[EUR][1000 genomes]
rs2169467	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2593211	0.83[EUR][1000 genomes]
rs2593249	0.83[EUR][1000 genomes]
rs2593250	0.83[EUR][1000 genomes]
rs2593252	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2703614	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2733333	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2733334	0.85[EUR][1000 genomes]
rs28372003	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28422021	0.80[EUR][1000 genomes]
rs28533433	0.81[EUR][1000 genomes]
rs28541606	0.80[EUR][1000 genomes]
rs28712697	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28781690	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6493900	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67077316	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7163267	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7169508	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7171073	0.81[EUR][1000 genomes]
rs7171304	0.80[EUR][1000 genomes]
rs7176873	0.80[EUR][1000 genomes]
rs8023736	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8034502	0.83[EUR][1000 genomes]
rs8035916	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9806170	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9806199	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs58479554	LOC283663	Cis_1M	lymphoblastoid	RTeQTL
rs58479554	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57353800-57406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:57372800-57410200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr15:57374800-57409600	Weak transcription	Osteobl	bone
4	chr15:57374800-57414600	Weak transcription	Fetal Kidney	kidney
5	chr15:57376200-57406000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr15:57381000-57412400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:57381200-57409400	Weak transcription	NHLF	lung
8	chr15:57382600-57423800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr15:57382800-57419600	Weak transcription	K562	blood
10	chr15:57384200-57409200	Weak transcription	Brain Germinal Matrix	brain
11	chr15:57384600-57405600	Weak transcription	Brain Anterior Caudate	brain
12	chr15:57384600-57410400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr15:57385200-57406200	Weak transcription	HepG2	liver
14	chr15:57386200-57410200	Weak transcription	Ovary	ovary
15	chr15:57386400-57426600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr15:57386600-57424600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr15:57386800-57405600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr15:57387000-57406400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:57387000-57430000	Weak transcription	Placenta	Placenta
20	chr15:57387200-57425400	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr15:57387400-57406000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr15:57387400-57406200	Weak transcription	HUVEC	blood vessel
23	chr15:57387600-57409400	Weak transcription	Dnd41	blood
24	chr15:57387600-57442400	Weak transcription	Fetal Intestine Large	intestine
25	chr15:57388200-57406200	Weak transcription	A549	lung
26	chr15:57390200-57409400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:57391200-57410200	Weak transcription	HMEC	breast
28	chr15:57391400-57409600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:57392600-57406000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr15:57392800-57406000	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr15:57394400-57406000	Weak transcription	Lung	lung
32	chr15:57397800-57416600	Weak transcription	Fetal Stomach	stomach
33	chr15:57398000-57415800	Weak transcription	Fetal Intestine Small	intestine
34	chr15:57399400-57406000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr15:57399400-57406200	Weak transcription	Adipose Nuclei	Adipose
36	chr15:57399400-57409200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:57399400-57409600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:57399400-57410000	Weak transcription	NH-A	brain
39	chr15:57399400-57424600	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr15:57399600-57406200	Weak transcription	Liver	Liver
41	chr15:57399600-57406400	Weak transcription	Fetal Lung	lung
42	chr15:57399600-57410000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:57399600-57410200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr15:57399600-57416200	Weak transcription	Primary T cells from cord blood	blood
45	chr15:57401600-57410200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:57402000-57410200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr15:57402600-57414600	Weak transcription	Primary B cells from cord blood	blood
48	chr15:57403000-57404800	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr15:57403000-57405600	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr15:57403000-57406000	Weak transcription	GM12878-XiMat	blood

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