Variant report

Variant	rs12900448
Chromosome Location	chr15:58798813-58798814
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	chr15:58797035..58800948-chr15:58803702..58808140,4	K562	blood:
2	chr15:58797460..58800451-chr15:58803881..58805523,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11071384	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12592017	0.89[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12898801	0.90[JPT][hapmap];0.85[MEX][hapmap];0.80[ASN][1000 genomes]
rs12898984	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1823697	1.00[YRI][hapmap]
rs1823698	1.00[YRI][hapmap]
rs1839929	1.00[YRI][hapmap]
rs1869144	0.90[JPT][hapmap];0.81[MEX][hapmap]
rs1869145	0.94[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1968688	1.00[YRI][hapmap]
rs1968690	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979177	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs2034613	1.00[YRI][hapmap]
rs2414588	0.84[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2899631	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3751543	0.81[AMR][1000 genomes]
rs4503731	1.00[YRI][hapmap]
rs4581653	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4774301	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775061	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775062	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775063	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4775064	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775065	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775066	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775067	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775068	1.00[YRI][hapmap]
rs57887591	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6494016	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66849766	0.92[EUR][1000 genomes]
rs7162786	0.80[ASN][1000 genomes]
rs7167672	1.00[YRI][hapmap]
rs7180936	1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7183248	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037479	1.00[YRI][hapmap]
rs8038906	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12900448	ADAM10	cis	lymphoblastoid	seeQTL
rs12900448	KIAA1370	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58791400-58809400	Weak transcription	Spleen	Spleen
2	chr15:58793400-58803400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:58795800-58799400	Enhancers	Fetal Thymus	thymus
4	chr15:58796400-58799400	Enhancers	Fetal Muscle Leg	muscle
5	chr15:58796400-58799600	Enhancers	Primary T cells from cord blood	blood
6	chr15:58797000-58799200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr15:58797200-58799000	Enhancers	Primary T cells fromperipheralblood	blood
8	chr15:58797200-58799000	Enhancers	Right Ventricle	heart
9	chr15:58797200-58799000	Enhancers	HSMM	muscle
10	chr15:58797200-58799200	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr15:58797200-58799200	Enhancers	Right Atrium	heart
12	chr15:58797400-58799200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr15:58797400-58799200	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr15:58797400-58799200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:58797400-58799200	Enhancers	Esophagus	oesophagus
16	chr15:58797400-58799600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr15:58797400-58799800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:58797400-58800000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr15:58797400-58800000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr15:58797600-58799000	Enhancers	Thymus	Thymus
21	chr15:58797600-58799200	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr15:58797600-58799400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:58797600-58799600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr15:58797600-58799800	Enhancers	HMEC	breast
25	chr15:58797800-58799000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr15:58797800-58799000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr15:58797800-58799000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:58797800-58799000	Enhancers	Duodenum Mucosa	Duodenum
29	chr15:58797800-58799400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
30	chr15:58798000-58799000	Enhancers	Placenta	Placenta
31	chr15:58798200-58799000	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr15:58798200-58799000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr15:58798200-58799000	Enhancers	Fetal Intestine Large	intestine
34	chr15:58798200-58799000	Enhancers	Psoas Muscle	Psoas
35	chr15:58798200-58799000	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr15:58798200-58799000	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr15:58798200-58799000	Enhancers	Stomach Mucosa	stomach
38	chr15:58798200-58799800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr15:58798400-58799000	Enhancers	Fetal Muscle Trunk	muscle
40	chr15:58798400-58799800	Weak transcription	K562	blood
41	chr15:58798600-58799000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr15:58798600-58799000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr15:58798600-58799400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr15:58798600-58799600	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr15:58798600-58799800	Enhancers	NHEK	skin
46	chr15:58798600-58807800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr15:58798600-58813200	Weak transcription	Aorta	Aorta
48	chr15:58798800-58799000	Enhancers	Hela-S3	cervix
49	chr15:58798800-58799200	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr15:58798800-58799200	Enhancers	HSMMtube	muscle

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