Variant report

Variant	rs35448466
Chromosome Location	chr8:52771964-52771965
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs13250133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13253956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13262316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13263610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13263767	0.87[AMR][1000 genomes]
rs13264394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13267912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13270817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13272813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13274476	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13277070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13279973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17196182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17196300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17196343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17210431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17210466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17282351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34011046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34070508	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34152859	0.87[AMR][1000 genomes]
rs34424720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34461077	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34724314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34837796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34934450	0.87[AMR][1000 genomes]
rs34949360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35025549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35038146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35098517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35254751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35314611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35822658	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35918180	0.87[AMR][1000 genomes]
rs35933421	0.87[AMR][1000 genomes]
rs36100144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71513545	0.81[AMR][1000 genomes]
rs71513547	0.87[AMR][1000 genomes]
rs71513550	0.87[AMR][1000 genomes]
rs71513551	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71513553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71513558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71513559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71513560	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71513562	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71513563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[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
rs35448466	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52733200-52783800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr8:52733800-52776400	Weak transcription	GM12878-XiMat	blood
3	chr8:52735600-52773400	Weak transcription	Brain Germinal Matrix	brain
4	chr8:52739800-52782600	Weak transcription	K562	blood
5	chr8:52759000-52786200	Weak transcription	Lung	lung
6	chr8:52759200-52786200	Weak transcription	Spleen	Spleen
7	chr8:52763800-52772600	Weak transcription	Fetal Kidney	kidney
8	chr8:52763800-52781800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr8:52764000-52774600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr8:52764000-52779400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr8:52764000-52781800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr8:52764000-52783600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr8:52764000-52793400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr8:52764200-52779000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr8:52764200-52782400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr8:52764400-52773400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr8:52764600-52776800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr8:52765400-52773600	Strong transcription	Fetal Thymus	thymus
19	chr8:52766000-52772200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr8:52766000-52772400	Weak transcription	HUVEC	blood vessel
21	chr8:52766000-52772600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr8:52766400-52775200	Weak transcription	Left Ventricle	heart
23	chr8:52766600-52772200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr8:52767400-52796600	Weak transcription	Fetal Brain Male	brain
25	chr8:52768000-52773800	Strong transcription	Dnd41	blood
26	chr8:52768200-52773600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr8:52768200-52773800	Strong transcription	Primary B cells from peripheral blood	blood
28	chr8:52768400-52773000	Enhancers	HMEC	breast
29	chr8:52768400-52774000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr8:52768600-52772600	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr8:52768600-52772800	Enhancers	Colon Smooth Muscle	Colon
32	chr8:52768600-52780200	Weak transcription	Fetal Intestine Small	intestine
33	chr8:52768800-52773600	Strong transcription	Primary T cells from cord blood	blood
34	chr8:52768800-52773600	Strong transcription	Primary hematopoietic stem cells	blood
35	chr8:52768800-52773800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr8:52769000-52773000	Strong transcription	Primary B cells from cord blood	blood
37	chr8:52769000-52773600	Strong transcription	Duodenum Mucosa	Duodenum
38	chr8:52769000-52774200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr8:52769000-52774200	Strong transcription	Fetal Intestine Large	intestine
40	chr8:52769200-52773200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr8:52769400-52772000	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr8:52769400-52773000	Strong transcription	Thymus	Thymus
43	chr8:52769400-52777600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr8:52769800-52781200	Weak transcription	Hela-S3	cervix
45	chr8:52769800-52782600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr8:52769800-52785200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr8:52769800-52793600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr8:52770200-52772000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr8:52770200-52772200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr8:52770200-52772600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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