Variant report

Variant	rs10097328
Chromosome Location	chr8:52742672-52742673
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	chr8:52742098..52744500-chr8:52748245..52750345,3	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10086504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10092494	0.97[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10096943	0.87[JPT][hapmap]
rs10102568	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10104368	0.83[ASN][1000 genomes]
rs10110304	0.82[JPT][hapmap]
rs1022317	0.86[JPT][hapmap]
rs10504127	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10504128	0.87[JPT][hapmap]
rs10504132	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1059041	0.86[JPT][hapmap]
rs1078888	0.87[JPT][hapmap]
rs10958299	0.87[JPT][hapmap]
rs10958308	0.81[CHB][hapmap]
rs11775601	0.87[JPT][hapmap]
rs11777885	0.94[JPT][hapmap]
rs11784921	0.88[JPT][hapmap]
rs12115132	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[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];0.98[ASN][1000 genomes]
rs1517305	0.87[JPT][hapmap]
rs16916800	0.85[ASN][1000 genomes]
rs16916878	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16916903	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16919843	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2020431	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2395857	0.86[JPT][hapmap]
rs28635761	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28652885	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3763547	0.81[JPT][hapmap]
rs3824266	0.87[JPT][hapmap]
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	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4873608	0.87[JPT][hapmap]
rs4873609	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4873613	0.87[JPT][hapmap]
rs5002416	0.82[JPT][hapmap]
rs56128832	0.87[EUR][1000 genomes]
rs56394995	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58408501	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58591247	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59344101	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs61196861	0.86[ASN][1000 genomes]
rs7008057	0.86[JPT][hapmap]
rs7008721	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7010217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7011046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7013587	0.87[JPT][hapmap]
rs7014075	0.87[JPT][hapmap]
rs7017450	0.87[JPT][hapmap]
rs73590413	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73592226	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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	0.97[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7829408	0.87[JPT][hapmap]
rs7835028	1.00[CEU][hapmap]
rs7843530	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[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]
rs9643465	0.83[YRI][hapmap]
rs9643466	0.86[JPT][hapmap]
rs9643792	0.87[JPT][hapmap]
rs9643793	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932026	chr8:51858658-52758574	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
rs10097328	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52722000-52771400	Weak transcription	Gastric	stomach
2	chr8:52722200-52752000	Weak transcription	Pancreas	Pancrea
3	chr8:52727600-52756800	Weak transcription	Brain Angular Gyrus	brain
4	chr8:52728200-52759200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr8:52731200-52763400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr8:52731200-52771000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr8:52731400-52753400	Weak transcription	NHDF-Ad	bronchial
8	chr8:52731800-52745600	Weak transcription	NHEK	skin
9	chr8:52732200-52743600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr8:52732200-52746000	Weak transcription	Fetal Brain Male	brain
11	chr8:52732200-52746400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr8:52732800-52753600	Weak transcription	Osteobl	bone
13	chr8:52733200-52758800	Weak transcription	Small Intestine	intestine
14	chr8:52733200-52763600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr8:52733200-52783800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr8:52733400-52757200	Weak transcription	Colonic Mucosa	Colon
17	chr8:52733600-52745200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr8:52733800-52776400	Weak transcription	GM12878-XiMat	blood
19	chr8:52734200-52761600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr8:52734400-52745200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr8:52735400-52744600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr8:52735400-52753400	Weak transcription	HUVEC	blood vessel
23	chr8:52735600-52753800	Weak transcription	HSMM	muscle
24	chr8:52735600-52763600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr8:52735600-52773400	Weak transcription	Brain Germinal Matrix	brain
26	chr8:52735800-52742800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr8:52735800-52753600	Weak transcription	Hela-S3	cervix
28	chr8:52735800-52763400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr8:52736000-52742800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr8:52736000-52753600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr8:52736000-52753600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr8:52736200-52753400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr8:52737200-52760400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr8:52737600-52753600	Weak transcription	NH-A	brain
35	chr8:52738200-52752000	Weak transcription	Right Atrium	heart
36	chr8:52738200-52753600	Weak transcription	A549	lung
37	chr8:52738400-52746200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr8:52738800-52746000	Strong transcription	Primary B cells from cord blood	blood
39	chr8:52738800-52746200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr8:52738800-52746200	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr8:52738800-52746200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr8:52739000-52744400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr8:52739000-52746000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr8:52739400-52746200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr8:52739600-52746000	Strong transcription	Liver	Liver
46	chr8:52739800-52747000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr8:52739800-52765400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr8:52739800-52782600	Weak transcription	K562	blood
49	chr8:52740000-52746000	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr8:52740200-52753400	Weak transcription	HMEC	breast

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