Variant report

Variant	rs4242479
Chromosome Location	chr8:52818658-52818659
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	chr8:52810071..52814912-chr8:52818559..52824033,9	MCF-7	breast:
2	chr8:52816572..52819580-chr8:52820038..52823147,3	K562	blood:

Variant related genes	Relation type
ENSG00000228801	Chromatin interaction
ENSG00000168300	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10086425	0.86[JPT][hapmap]
rs10086504	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs10101163	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10105030	0.86[JPT][hapmap]
rs1013621	0.86[JPT][hapmap]
rs1013622	0.86[JPT][hapmap]
rs10958304	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10958305	0.85[EUR][1000 genomes]
rs11774370	0.86[JPT][hapmap]
rs11775587	0.82[EUR][1000 genomes]
rs11775611	0.85[EUR][1000 genomes]
rs11784869	0.81[EUR][1000 genomes]
rs11787499	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12335014	0.85[JPT][hapmap]
rs12681734	0.82[EUR][1000 genomes]
rs13265006	0.80[EUR][1000 genomes]
rs1517306	0.85[JPT][hapmap]
rs16916858	0.85[JPT][hapmap]
rs16916952	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16916966	0.96[YRI][hapmap]
rs2176121	0.86[JPT][hapmap]
rs34058697	0.82[EUR][1000 genomes]
rs34372756	0.85[EUR][1000 genomes]
rs35032384	0.83[EUR][1000 genomes]
rs4565453	0.85[JPT][hapmap]
rs6473660	0.86[JPT][hapmap]
rs6986544	0.86[JPT][hapmap]
rs7010217	0.87[LWK][hapmap]
rs71513561	0.82[EUR][1000 genomes]
rs7462096	0.86[JPT][hapmap]
rs7814421	0.86[JPT][hapmap]
rs925762	0.86[JPT][hapmap]
rs9298462	0.86[JPT][hapmap]
rs9643465	0.85[LWK][hapmap]
rs9650179	0.85[EUR][1000 genomes]
rs9650180	0.84[EUR][1000 genomes]
rs9650305	0.85[EUR][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
rs4242479	PCMTD1	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52812800-52822200	Weak transcription	Esophagus	oesophagus
2	chr8:52812800-52827800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:52812800-52833400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr8:52813200-52822200	Weak transcription	Aorta	Aorta
5	chr8:52813200-52831000	Weak transcription	Right Ventricle	heart
6	chr8:52813200-52833200	Weak transcription	Brain Angular Gyrus	brain
7	chr8:52813400-52826800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr8:52813400-52827000	Weak transcription	Fetal Intestine Large	intestine
9	chr8:52813400-52829000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr8:52813400-52829200	Weak transcription	Brain Anterior Caudate	brain
11	chr8:52813400-52837200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr8:52813600-52837400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr8:52813800-52831600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr8:52813800-52831600	Weak transcription	Fetal Stomach	stomach
15	chr8:52813800-52833200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr8:52813800-52835800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr8:52813800-52837400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr8:52814000-52833200	Weak transcription	Fetal Lung	lung
19	chr8:52814000-52833600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr8:52814000-52836200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr8:52814000-52837400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr8:52814000-52839200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr8:52814200-52821200	Weak transcription	Thymus	Thymus
24	chr8:52814200-52842000	Weak transcription	Brain Substantia Nigra	brain
25	chr8:52814200-52850000	Weak transcription	Spleen	Spleen
26	chr8:52814800-52818800	Weak transcription	Psoas Muscle	Psoas
27	chr8:52814800-52821800	Weak transcription	Fetal Intestine Small	intestine
28	chr8:52814800-52829600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr8:52814800-52834200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr8:52814800-52834600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr8:52814800-52837200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr8:52815000-52852000	Weak transcription	Colon Smooth Muscle	Colon
33	chr8:52815200-52821400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr8:52815200-52823600	Weak transcription	Adipose Nuclei	Adipose
35	chr8:52815200-52827200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr8:52815200-52828400	Weak transcription	Dnd41	blood
37	chr8:52815200-52833000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr8:52815200-52837400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr8:52815400-52822000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr8:52816000-52819600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr8:52816200-52820800	Weak transcription	GM12878-XiMat	blood
42	chr8:52816200-52822000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr8:52816200-52822000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr8:52816200-52822200	Weak transcription	Primary B cells from cord blood	blood
45	chr8:52816200-52831000	Weak transcription	Primary T cells from cord blood	blood
46	chr8:52816400-52823200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr8:52816800-52819000	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr8:52817000-52821200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr8:52817000-52821400	Weak transcription	Primary B cells from peripheral blood	blood
50	chr8:52817200-52822200	Weak transcription	Fetal Muscle Leg	muscle

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