Variant report

Variant	rs10086504
Chromosome Location	chr8:52822520-52822521
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:52816572..52819580-chr8:52820038..52823147,3	K562	blood:
2	chr8:52810071..52814912-chr8:52818559..52824033,9	MCF-7	breast:
3	chr8:52812069..52813653-chr8:52821954..52824143,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168300	Chromatin interaction
ENSG00000228801	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10092494	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10096943	0.87[JPT][hapmap]
rs10097328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10101163	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs10102568	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10110304	0.82[JPT][hapmap]
rs1022317	0.86[JPT][hapmap]
rs10504127	0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10504128	0.87[JPT][hapmap]
rs10504132	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1059041	0.86[JPT][hapmap]
rs1078888	0.87[JPT][hapmap]
rs10958299	0.87[JPT][hapmap]
rs10958308	0.80[CHB][hapmap];0.92[EUR][1000 genomes]
rs11775601	0.87[JPT][hapmap]
rs11777885	0.94[JPT][hapmap]
rs11784921	0.88[JPT][hapmap]
rs11787499	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs11992148	0.92[EUR][1000 genomes]
rs12115132	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12678479	0.86[JPT][hapmap]
rs13250860	0.86[JPT][hapmap]
rs13257067	0.87[JPT][hapmap]
rs13257291	0.87[JPT][hapmap]
rs13261243	0.87[JPT][hapmap]
rs13275235	0.87[JPT][hapmap]
rs13281179	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1517305	0.87[JPT][hapmap]
rs16916878	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16916903	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16916952	0.96[YRI][hapmap]
rs16916966	0.96[YRI][hapmap]
rs16916974	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16916979	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16917021	0.92[EUR][1000 genomes]
rs16917071	0.92[EUR][1000 genomes]
rs16917074	0.92[EUR][1000 genomes]
rs16917075	0.92[EUR][1000 genomes]
rs16919843	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2020431	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2090258	0.92[EUR][1000 genomes]
rs2395857	0.86[JPT][hapmap]
rs28635761	0.88[AMR][1000 genomes]
rs28652885	0.88[AMR][1000 genomes]
rs28754887	0.85[ASN][1000 genomes]
rs3763547	0.81[JPT][hapmap]
rs3824266	0.87[JPT][hapmap]
rs4242479	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs4259408	0.87[JPT][hapmap]
rs4294173	0.86[JPT][hapmap]
rs4324911	0.86[JPT][hapmap]
rs4330683	0.87[JPT][hapmap]
rs4361755	0.87[JPT][hapmap]
rs4570148	0.86[JPT][hapmap]
rs4584139	0.87[JPT][hapmap]
rs4587320	0.86[JPT][hapmap]
rs4596648	0.87[JPT][hapmap]
rs4612332	0.87[JPT][hapmap]
rs4618684	0.86[JPT][hapmap]
rs4634632	0.87[JPT][hapmap]
rs4873602	0.88[AMR][1000 genomes]
rs4873608	0.87[JPT][hapmap]
rs4873609	0.97[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4873613	0.87[JPT][hapmap]
rs4873623	0.92[EUR][1000 genomes]
rs5002416	0.82[JPT][hapmap]
rs55713338	0.92[EUR][1000 genomes]
rs56275645	0.92[EUR][1000 genomes]
rs56394995	0.97[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs57745642	0.92[EUR][1000 genomes]
rs58408501	0.91[AMR][1000 genomes]
rs58591247	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs59344101	0.82[AMR][1000 genomes]
rs59734823	0.92[EUR][1000 genomes]
rs61196861	0.95[ASN][1000 genomes]
rs61262162	0.92[EUR][1000 genomes]
rs7008057	0.86[JPT][hapmap]
rs7008721	0.88[AMR][1000 genomes]
rs7009037	0.92[EUR][1000 genomes]
rs7010217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7011046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7013587	0.87[JPT][hapmap]
rs7014075	0.87[JPT][hapmap]
rs7017450	0.87[JPT][hapmap]
rs73590413	0.88[AMR][1000 genomes]
rs73592226	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7460311	0.87[JPT][hapmap]
rs7463120	0.87[JPT][hapmap]
rs7464192	0.87[JPT][hapmap]
rs7465225	0.86[JPT][hapmap]
rs753540	0.86[JPT][hapmap]
rs7815751	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7829408	0.87[JPT][hapmap]
rs7843530	0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs882492	0.87[JPT][hapmap]
rs884580	0.87[JPT][hapmap]
rs925763	0.87[JPT][hapmap]
rs9298463	0.86[JPT][hapmap]
rs9298464	0.86[JPT][hapmap]
rs9298466	0.87[JPT][hapmap]
rs9298467	0.81[JPT][hapmap]
rs950687	0.87[JPT][hapmap]
rs9643466	0.86[JPT][hapmap]
rs9643792	0.87[JPT][hapmap]
rs9643793	0.87[JPT][hapmap]

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
rs10086504	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52812800-52827800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:52812800-52833400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr8:52813200-52831000	Weak transcription	Right Ventricle	heart
4	chr8:52813200-52833200	Weak transcription	Brain Angular Gyrus	brain
5	chr8:52813400-52826800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr8:52813400-52827000	Weak transcription	Fetal Intestine Large	intestine
7	chr8:52813400-52829000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr8:52813400-52829200	Weak transcription	Brain Anterior Caudate	brain
9	chr8:52813400-52837200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr8:52813600-52837400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr8:52813800-52831600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr8:52813800-52831600	Weak transcription	Fetal Stomach	stomach
13	chr8:52813800-52833200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr8:52813800-52835800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr8:52813800-52837400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr8:52814000-52833200	Weak transcription	Fetal Lung	lung
17	chr8:52814000-52833600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr8:52814000-52836200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr8:52814000-52837400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr8:52814000-52839200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr8:52814200-52842000	Weak transcription	Brain Substantia Nigra	brain
22	chr8:52814200-52850000	Weak transcription	Spleen	Spleen
23	chr8:52814800-52829600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr8:52814800-52834200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr8:52814800-52834600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr8:52814800-52837200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr8:52815000-52852000	Weak transcription	Colon Smooth Muscle	Colon
28	chr8:52815200-52823600	Weak transcription	Adipose Nuclei	Adipose
29	chr8:52815200-52827200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr8:52815200-52828400	Weak transcription	Dnd41	blood
31	chr8:52815200-52833000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr8:52815200-52837400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr8:52816200-52831000	Weak transcription	Primary T cells from cord blood	blood
34	chr8:52816400-52823200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr8:52817200-52827800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr8:52817200-52830800	Weak transcription	Left Ventricle	heart
37	chr8:52817200-52830800	Weak transcription	Ovary	ovary
38	chr8:52817200-52833400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr8:52817800-52831000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr8:52818000-52834800	Weak transcription	Pancreas	Pancrea
41	chr8:52819400-52834200	Weak transcription	Psoas Muscle	Psoas
42	chr8:52820200-52826600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr8:52821200-52823600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr8:52821200-52826600	Weak transcription	Liver	Liver
45	chr8:52821400-52822600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr8:52821400-52823000	Strong transcription	Thymus	Thymus
47	chr8:52821800-52823000	ZNF genes & repeats	Fetal Intestine Small	intestine
48	chr8:52822000-52823000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
49	chr8:52822200-52822600	ZNF genes & repeats	Fetal Muscle Leg	muscle
50	chr8:52822200-52822800	ZNF genes & repeats	Primary B cells from cord blood	blood

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