Variant report

Variant	rs60304457
Chromosome Location	chr8:52836101-52836102
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	chr8:52811802..52816093-chr8:52833537..52836202,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228801	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10504130	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10958300	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10958301	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10958305	1.00[ASN][1000 genomes]
rs11775587	1.00[ASN][1000 genomes]
rs11775611	1.00[ASN][1000 genomes]
rs11777016	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11777714	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11778849	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11780040	0.96[ASN][1000 genomes]
rs11780891	0.81[AMR][1000 genomes]
rs11781330	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11784869	1.00[ASN][1000 genomes]
rs11785805	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11786167	0.81[AMR][1000 genomes]
rs11787229	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12675786	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12675907	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12676345	0.84[ASN][1000 genomes]
rs12676780	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12676835	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12677407	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12678639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12679287	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12679983	0.83[ASN][1000 genomes]
rs12680128	0.83[ASN][1000 genomes]
rs12681203	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12681734	0.96[ASN][1000 genomes]
rs13265006	0.96[ASN][1000 genomes]
rs13276400	0.84[ASN][1000 genomes]
rs16916820	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16916856	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16916865	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16916906	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16916961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17212214	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17212256	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17284746	1.00[ASN][1000 genomes]
rs2037138	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2037139	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2069119	0.84[ASN][1000 genomes]
rs2176120	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34058697	0.94[ASN][1000 genomes]
rs34073804	0.85[ASN][1000 genomes]
rs34213209	0.84[ASN][1000 genomes]
rs34319820	0.85[ASN][1000 genomes]
rs34364864	0.94[ASN][1000 genomes]
rs34372756	1.00[ASN][1000 genomes]
rs34677273	1.00[ASN][1000 genomes]
rs34973406	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35032384	1.00[ASN][1000 genomes]
rs35509250	0.84[ASN][1000 genomes]
rs35603537	0.84[ASN][1000 genomes]
rs41453644	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4292674	0.83[ASN][1000 genomes]
rs4321994	0.82[ASN][1000 genomes]
rs4534123	0.83[ASN][1000 genomes]
rs4598243	0.91[ASN][1000 genomes]
rs4626585	0.83[ASN][1000 genomes]
rs57212480	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58561048	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58583070	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59602923	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60153173	0.85[ASN][1000 genomes]
rs60796336	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61326367	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6994203	0.94[ASN][1000 genomes]
rs71513549	0.83[ASN][1000 genomes]
rs71513552	0.85[ASN][1000 genomes]
rs71513561	0.96[ASN][1000 genomes]
rs71513564	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs763550	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9650179	1.00[ASN][1000 genomes]
rs9650180	1.00[ASN][1000 genomes]
rs9650305	1.00[ASN][1000 genomes]
rs9792352	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[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
rs60304457	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52813400-52837200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr8:52813600-52837400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr8:52813800-52837400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr8:52814000-52836200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr8:52814000-52837400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr8:52814000-52839200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr8:52814200-52842000	Weak transcription	Brain Substantia Nigra	brain
8	chr8:52814200-52850000	Weak transcription	Spleen	Spleen
9	chr8:52814800-52837200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr8:52815000-52852000	Weak transcription	Colon Smooth Muscle	Colon
11	chr8:52815200-52837400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr8:52822400-52837800	Weak transcription	Esophagus	oesophagus
13	chr8:52822600-52860200	Weak transcription	Fetal Muscle Leg	muscle
14	chr8:52823000-52840200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr8:52823600-52838200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr8:52827600-52836600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr8:52831200-52838800	Weak transcription	Left Ventricle	heart
18	chr8:52831200-52840800	Weak transcription	Right Ventricle	heart
19	chr8:52831400-52836200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr8:52831600-52837200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr8:52831800-52841000	Weak transcription	Lung	lung
22	chr8:52831800-52858400	Weak transcription	Primary T cells from cord blood	blood
23	chr8:52831800-52863400	Weak transcription	Aorta	Aorta
24	chr8:52832000-52836400	Weak transcription	Fetal Stomach	stomach
25	chr8:52832000-52838400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr8:52835200-52837600	Weak transcription	Pancreas	Pancrea
27	chr8:52835400-52837200	Weak transcription	Primary B cells from cord blood	blood
28	chr8:52835400-52837800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr8:52835400-52840200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr8:52835600-52837400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr8:52835600-52837400	Weak transcription	Psoas Muscle	Psoas
32	chr8:52835800-52836400	Strong transcription	Ovary	ovary
33	chr8:52835800-52836800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
34	chr8:52835800-52837000	ZNF genes & repeats	Fetal Intestine Small	intestine
35	chr8:52835800-52837800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr8:52836000-52837200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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