Variant report

Variant	rs12915116
Chromosome Location	chr15:43074680-43074681
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	chr15:43067614..43069309-chr15:43072261..43074765,2	K562	blood:
2	chr15:43073320..43075006-chr15:43078502..43081178,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1058846	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902830	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905385	0.82[MEX][hapmap];0.80[EUR][1000 genomes]
rs12908349	1.00[ASN][1000 genomes]
rs12910799	1.00[ASN][1000 genomes]
rs12911334	1.00[ASN][1000 genomes]
rs12911585	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs12913618	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12914380	1.00[ASN][1000 genomes]
rs17774047	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2136899	0.84[CEU][hapmap];0.91[MEX][hapmap];0.80[EUR][1000 genomes]
rs2175370	0.84[CEU][hapmap]
rs34745458	1.00[ASN][1000 genomes]
rs35088691	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35202249	1.00[ASN][1000 genomes]
rs35298309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35326878	1.00[ASN][1000 genomes]
rs35392023	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35538776	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs36092914	1.00[ASN][1000 genomes]
rs3742993	0.84[CEU][hapmap];0.82[MEX][hapmap]
rs4545789	0.84[CEU][hapmap]
rs4923954	1.00[ASN][1000 genomes]
rs4924692	0.84[CEU][hapmap]
rs4924694	0.83[CEU][hapmap];0.91[MEX][hapmap];0.80[EUR][1000 genomes]
rs4924699	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs61122145	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66681258	0.81[EUR][1000 genomes]
rs66932813	1.00[ASN][1000 genomes]
rs672054	0.84[CEU][hapmap]
rs7166373	0.84[CEU][hapmap]
rs7175582	0.85[CEU][hapmap]
rs7176860	0.80[EUR][1000 genomes]
rs7182141	0.85[CEU][hapmap]
rs72713784	1.00[ASN][1000 genomes]
rs72713795	1.00[ASN][1000 genomes]
rs72719486	1.00[ASN][1000 genomes]
rs72721511	1.00[ASN][1000 genomes]
rs8024902	0.84[CEU][hapmap]
rs8031218	0.91[MEX][hapmap]
rs8037613	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8039711	0.84[CEU][hapmap]
rs8039765	0.84[CEU][hapmap];0.91[MEX][hapmap]
rs938047	0.84[CEU][hapmap]

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	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv977054	chr15:43015821-43171355	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1050128	chr15:43056145-43262736	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv542368	chr15:43056145-43262736	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12915116	BUB1B	cis	parietal	SCAN
rs12915116	MAP1A	cis	parietal	SCAN
rs12915116	CDAN1	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43030000-43093600	Weak transcription	Colonic Mucosa	Colon
2	chr15:43051800-43075000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:43051800-43083800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:43053600-43112200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr15:43054000-43080200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr15:43054800-43146000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr15:43056800-43116800	Weak transcription	HepG2	liver
8	chr15:43057600-43107000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr15:43060800-43122200	Weak transcription	GM12878-XiMat	blood
10	chr15:43062600-43087800	Weak transcription	K562	blood
11	chr15:43062800-43075200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr15:43062800-43088600	Weak transcription	NHDF-Ad	bronchial
13	chr15:43063000-43083200	Weak transcription	Fetal Intestine Small	intestine
14	chr15:43063000-43093000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:43063400-43093600	Weak transcription	Esophagus	oesophagus
16	chr15:43063400-43136200	Weak transcription	Psoas Muscle	Psoas
17	chr15:43064000-43114200	Weak transcription	Fetal Kidney	kidney
18	chr15:43064200-43075000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:43064800-43074800	Weak transcription	Brain Substantia Nigra	brain
20	chr15:43064800-43150800	Weak transcription	HSMM	muscle
21	chr15:43066200-43074800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr15:43066400-43095600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr15:43066600-43088600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr15:43066600-43097600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr15:43067400-43147200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr15:43067600-43074800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr15:43067600-43078400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:43067600-43092800	Weak transcription	Brain Germinal Matrix	brain
29	chr15:43067800-43074800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr15:43067800-43093000	Weak transcription	Fetal Brain Female	brain
31	chr15:43067800-43095200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:43068000-43074800	Weak transcription	Osteobl	bone
33	chr15:43068000-43075000	Weak transcription	Thymus	Thymus
34	chr15:43068000-43075200	Weak transcription	Lung	lung
35	chr15:43068000-43077800	Weak transcription	HMEC	breast
36	chr15:43068000-43093000	Weak transcription	Spleen	Spleen
37	chr15:43068200-43075000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr15:43068400-43074800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr15:43068400-43075000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr15:43068400-43089200	Weak transcription	HUVEC	blood vessel
41	chr15:43068400-43093000	Weak transcription	Aorta	Aorta
42	chr15:43068400-43093600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr15:43068600-43074800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr15:43068800-43075000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr15:43068800-43075000	Weak transcription	NHEK	skin
46	chr15:43068800-43077000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr15:43068800-43089600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr15:43068800-43092600	Weak transcription	Brain Hippocampus Middle	brain
49	chr15:43069000-43075000	Weak transcription	Adipose Nuclei	Adipose
50	chr15:43069000-43075000	Weak transcription	Rectal Mucosa Donor 29	rectum

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