Variant report

Variant	rs12324526
Chromosome Location	chr15:57904826-57904827
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	chr15:57851773..57853797-chr15:57903678..57905009,17	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1009319	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10152310	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10152878	1.00[ASN][1000 genomes]
rs10851618	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10851619	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11071335	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];1.00[ASN][1000 genomes]
rs11852838	1.00[ASN][1000 genomes]
rs11853270	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11856824	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12323998	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12324010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324289	0.92[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12442978	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12442987	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];1.00[ASN][1000 genomes]
rs12443389	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12443485	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13380406	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13380418	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1346125	1.00[ASN][1000 genomes]
rs16977630	1.00[CHB][hapmap]
rs17239937	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17820515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];1.00[ASN][1000 genomes]
rs2172608	1.00[ASN][1000 genomes]
rs28557258	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774273	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4774274	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4774281	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4774282	1.00[ASN][1000 genomes]
rs4774971	1.00[ASN][1000 genomes]
rs4774974	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57589057	1.00[ASN][1000 genomes]
rs58017146	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58919063	1.00[ASN][1000 genomes]
rs61600143	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7178159	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];1.00[ASN][1000 genomes]
rs72743512	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72743516	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72745565	1.00[ASN][1000 genomes]
rs7359330	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs74016366	1.00[ASN][1000 genomes]
rs9796502	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[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	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
2	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv904255	chr15:57790436-57907574	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12324526	PAPD7	trans	cerebellum	SCAN
rs12324526	DMXL2	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57892000-57908800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:57894400-57938200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr15:57897000-57909200	Weak transcription	Psoas Muscle	Psoas
4	chr15:57899000-57905000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr15:57899200-57905000	Enhancers	Duodenum Mucosa	Duodenum
6	chr15:57899200-57905200	Enhancers	Fetal Heart	heart
7	chr15:57900600-57905200	Enhancers	Fetal Intestine Large	intestine
8	chr15:57900600-57911800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:57900600-57941600	Weak transcription	Colonic Mucosa	Colon
10	chr15:57901200-57905000	Enhancers	Colon Smooth Muscle	Colon
11	chr15:57901600-57905000	Enhancers	Fetal Intestine Small	intestine
12	chr15:57901800-57912000	Weak transcription	Spleen	Spleen
13	chr15:57902600-57907800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr15:57903000-57907600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr15:57903000-57907800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr15:57903200-57905000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr15:57903200-57907600	Weak transcription	Esophagus	oesophagus
18	chr15:57903400-57905000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr15:57903600-57905000	Enhancers	HMEC	breast
20	chr15:57904200-57906000	Weak transcription	HepG2	liver
21	chr15:57904400-57905000	Enhancers	Right Atrium	heart
22	chr15:57904400-57935200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr15:57904600-57905000	Enhancers	Stomach Mucosa	stomach
24	chr15:57904600-57905000	Enhancers	Hela-S3	cervix
25	chr15:57904600-57906000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:57904600-57906400	Weak transcription	Left Ventricle	heart
27	chr15:57904600-57906400	Weak transcription	Lung	lung
28	chr15:57904600-57906400	Weak transcription	Pancreas	Pancrea
29	chr15:57904600-57906400	Weak transcription	Right Ventricle	heart
30	chr15:57904600-57907200	Weak transcription	Adipose Nuclei	Adipose
31	chr15:57904600-57907600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr15:57904600-57910600	Weak transcription	Gastric	stomach
33	chr15:57904600-57914800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr15:57904600-57918000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr15:57904600-57919000	Weak transcription	Fetal Lung	lung
36	chr15:57904600-57919000	Weak transcription	Fetal Muscle Leg	muscle
37	chr15:57904600-57919200	Weak transcription	Ovary	ovary
38	chr15:57904600-57921600	Weak transcription	Fetal Stomach	stomach
39	chr15:57904600-57936400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:57904800-57905000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr15:57904800-57906800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr15:57904800-57910000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr15:57904800-57910800	Weak transcription	HUVEC	blood vessel
44	chr15:57904800-57919000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr15:57904800-57919000	Weak transcription	Fetal Kidney	kidney

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