Variant report

Variant	rs12459015
Chromosome Location	chr19:38083189-38083190
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38081627..38083725-chr19:38083732..38085757,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171817	Chromatin interaction
ENSG00000180479	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10402671	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10403173	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10404031	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10406379	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10408619	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10409605	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10410588	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10412510	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10412786	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10417576	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10420268	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10420552	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10425795	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12979640	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13744	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1531549	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1564206	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1564208	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16958861	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16958863	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1975937	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1975939	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2075284	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2287229	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2291002	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28512414	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2909085	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2909088	0.84[ASN][1000 genomes]
rs2909093	0.80[ASN][1000 genomes]
rs2909098	0.80[ASN][1000 genomes]
rs2909102	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2909105	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2909109	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2927739	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2927740	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2927742	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2927746	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2927747	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2972430	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2972434	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2972446	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2972447	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2972448	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2972452	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2972458	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3101746	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3101747	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3112433	0.80[ASN][1000 genomes]
rs35863684	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3829688	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4802024	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4802029	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803215	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4803231	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4803233	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4803262	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803263	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803276	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803287	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56151076	0.84[ASN][1000 genomes]
rs6508736	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8100646	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8103647	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8110865	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9304568	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs954504	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs968073	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9749368	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9797618	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9941475	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12459015	ZNF571	cis	multi-tissue	Pritchard

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38069800-38084600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:38072400-38084600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr19:38075200-38084600	Weak transcription	Fetal Heart	heart
4	chr19:38077200-38084600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:38078200-38084400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr19:38078200-38084600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr19:38078200-38084600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr19:38078600-38084600	Weak transcription	Thymus	Thymus
9	chr19:38078800-38084600	Weak transcription	Colonic Mucosa	Colon
10	chr19:38079600-38083200	Weak transcription	Psoas Muscle	Psoas
11	chr19:38079600-38083600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr19:38079600-38084600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr19:38079600-38084600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr19:38080000-38084400	Weak transcription	Left Ventricle	heart
15	chr19:38080200-38084600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr19:38080400-38084600	Weak transcription	Small Intestine	intestine
17	chr19:38080600-38084400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr19:38081600-38084400	Weak transcription	Placenta	Placenta
19	chr19:38082000-38083200	ZNF genes & repeats	Primary T cells from cord blood	blood
20	chr19:38082000-38083800	ZNF genes & repeats	Liver	Liver
21	chr19:38082000-38084000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:38082000-38084000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
23	chr19:38082200-38083400	Weak transcription	Brain Substantia Nigra	brain
24	chr19:38082400-38083200	Weak transcription	Fetal Lung	lung
25	chr19:38082400-38083600	Weak transcription	Brain Hippocampus Middle	brain
26	chr19:38082400-38084400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr19:38082400-38084600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:38082400-38084600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr19:38082400-38084600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr19:38082600-38083200	ZNF genes & repeats	Fetal Stomach	stomach
31	chr19:38082800-38084000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
32	chr19:38082800-38084600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr19:38083000-38083600	ZNF genes & repeats	Fetal Kidney	kidney
34	chr19:38083000-38083800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
35	chr19:38083000-38084000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr19:38083000-38084600	Weak transcription	HSMMtube	muscle

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