Variant report

Variant	rs12545881
Chromosome Location	chr8:52828214-52828215
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	chr16:3073094..3075492-chr8:52827901..52830153,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131652	Chromatin interaction
ENSG00000103145	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11551686	1.00[ASN][1000 genomes]
rs12541846	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12543540	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12544903	1.00[ASN][1000 genomes]
rs12545812	0.93[ASN][1000 genomes]
rs28451175	1.00[ASN][1000 genomes]
rs56117807	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6473665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6982992	1.00[JPT][hapmap]
rs6993171	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7015360	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73583651	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73583663	0.93[ASN][1000 genomes]
rs7819631	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9643465	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1018429	chr8:52411443-52878946	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1034856	chr8:52411443-52886765	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Bivalent Enhancer 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	19 gene(s)	inside rSNPs	diseases
4	nsv831316	chr8:52660353-52842928	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12545881	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52812800-52833400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr8:52813200-52831000	Weak transcription	Right Ventricle	heart
3	chr8:52813200-52833200	Weak transcription	Brain Angular Gyrus	brain
4	chr8:52813400-52829000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr8:52813400-52829200	Weak transcription	Brain Anterior Caudate	brain
6	chr8:52813400-52837200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr8:52813600-52837400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr8:52813800-52831600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr8:52813800-52831600	Weak transcription	Fetal Stomach	stomach
10	chr8:52813800-52833200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr8:52813800-52835800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr8:52813800-52837400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr8:52814000-52833200	Weak transcription	Fetal Lung	lung
14	chr8:52814000-52833600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr8:52814000-52836200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr8:52814000-52837400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr8:52814000-52839200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr8:52814200-52842000	Weak transcription	Brain Substantia Nigra	brain
19	chr8:52814200-52850000	Weak transcription	Spleen	Spleen
20	chr8:52814800-52829600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr8:52814800-52834200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr8:52814800-52834600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr8:52814800-52837200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr8:52815000-52852000	Weak transcription	Colon Smooth Muscle	Colon
25	chr8:52815200-52828400	Weak transcription	Dnd41	blood
26	chr8:52815200-52833000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr8:52815200-52837400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr8:52816200-52831000	Weak transcription	Primary T cells from cord blood	blood
29	chr8:52817200-52830800	Weak transcription	Left Ventricle	heart
30	chr8:52817200-52830800	Weak transcription	Ovary	ovary
31	chr8:52817200-52833400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr8:52817800-52831000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr8:52818000-52834800	Weak transcription	Pancreas	Pancrea
34	chr8:52819400-52834200	Weak transcription	Psoas Muscle	Psoas
35	chr8:52822400-52837800	Weak transcription	Esophagus	oesophagus
36	chr8:52822600-52860200	Weak transcription	Fetal Muscle Leg	muscle
37	chr8:52823000-52830000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr8:52823000-52830800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr8:52823000-52833600	Weak transcription	Thymus	Thymus
40	chr8:52823000-52834800	Weak transcription	Fetal Intestine Small	intestine
41	chr8:52823000-52840200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr8:52823600-52838200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr8:52824200-52831600	Weak transcription	Aorta	Aorta
44	chr8:52824800-52832600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr8:52825600-52829000	Weak transcription	Brain Hippocampus Middle	brain
46	chr8:52826600-52828400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr8:52826800-52834800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr8:52827000-52828800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr8:52827200-52833600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr8:52827400-52830800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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