Variant report

Variant	rs1869144
Chromosome Location	chr15:58797300-58797301
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:58797035..58800948-chr15:58803702..58808140,4	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12324517	0.86[JPT][hapmap]
rs12592017	0.80[MEX][hapmap]
rs12898801	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12898984	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs12900448	0.90[JPT][hapmap];0.81[MEX][hapmap]
rs1869145	0.90[JPT][hapmap];0.81[MEX][hapmap];0.81[ASN][1000 genomes]
rs1968690	0.90[JPT][hapmap]
rs2414588	0.90[JPT][hapmap];0.81[MEX][hapmap];0.80[ASN][1000 genomes]
rs2899631	0.90[JPT][hapmap]
rs4774301	0.90[JPT][hapmap];0.85[MEX][hapmap]
rs4774302	0.88[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4775061	0.90[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes]
rs4775062	0.90[JPT][hapmap];0.85[MEX][hapmap]
rs4775064	0.89[JPT][hapmap]
rs4775065	0.90[JPT][hapmap];0.85[MEX][hapmap]
rs4775067	0.90[JPT][hapmap]
rs6494016	0.81[ASN][1000 genomes]
rs7162786	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72743015	0.83[EUR][1000 genomes]
rs8038906	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3362898	chr15:58705732-58850860	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1043041	chr15:58744505-58876327	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv904268	chr15:58763678-58803225	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1869144	KIAA1370	cis	cerebellum	SCAN
rs1869144	TCF12	cis	cerebellum	SCAN
rs1869144	CA2	trans	lymphoblastoid	seeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58784000-58797800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:58791400-58797400	Weak transcription	Esophagus	oesophagus
3	chr15:58791400-58809400	Weak transcription	Spleen	Spleen
4	chr15:58791600-58797600	Weak transcription	HMEC	breast
5	chr15:58792000-58797400	Weak transcription	NHEK	skin
6	chr15:58792400-58797400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:58792400-58797600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr15:58792600-58797800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:58792800-58797400	Weak transcription	NHDF-Ad	bronchial
10	chr15:58793400-58803400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:58794600-58797400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr15:58794600-58798000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr15:58794600-58798000	Weak transcription	Placenta	Placenta
14	chr15:58795200-58797400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:58795600-58797600	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr15:58795600-58797600	Enhancers	HSMMtube	muscle
17	chr15:58795600-58798200	Weak transcription	Fetal Intestine Large	intestine
18	chr15:58795600-58798200	Weak transcription	Fetal Intestine Small	intestine
19	chr15:58795800-58797800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr15:58795800-58799400	Enhancers	Fetal Thymus	thymus
21	chr15:58796000-58798000	Weak transcription	Lung	lung
22	chr15:58796000-58798200	Weak transcription	Psoas Muscle	Psoas
23	chr15:58796000-58798200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:58796000-58798200	Weak transcription	Stomach Mucosa	stomach
25	chr15:58796000-58798400	Enhancers	GM12878-XiMat	blood
26	chr15:58796200-58797600	Weak transcription	Thymus	Thymus
27	chr15:58796400-58797600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr15:58796400-58799400	Enhancers	Fetal Muscle Leg	muscle
29	chr15:58796400-58799600	Enhancers	Primary T cells from cord blood	blood
30	chr15:58796800-58798000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr15:58797000-58797400	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr15:58797000-58797800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr15:58797000-58798800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:58797000-58798800	Enhancers	Left Ventricle	heart
35	chr15:58797000-58799200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:58797200-58798400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr15:58797200-58798800	Enhancers	Placenta Amnion	Placenta Amnion
38	chr15:58797200-58799000	Enhancers	Primary T cells fromperipheralblood	blood
39	chr15:58797200-58799000	Enhancers	Right Ventricle	heart
40	chr15:58797200-58799000	Enhancers	HSMM	muscle
41	chr15:58797200-58799200	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr15:58797200-58799200	Enhancers	Right Atrium	heart

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