Variant report

Variant	rs41453644
Chromosome Location	chr8:52733544-52733545
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10087958	0.82[JPT][hapmap]
rs10504130	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10958300	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10958301	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10958305	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs11775587	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs11775611	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs11777016	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11777714	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11778849	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11780040	0.96[ASN][1000 genomes]
rs11780891	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs11781330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11784869	0.93[ASN][1000 genomes]
rs11785805	0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs11786167	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11787229	0.85[ASN][1000 genomes]
rs12675786	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12675907	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12676345	0.91[ASN][1000 genomes]
rs12676780	0.92[ASN][1000 genomes]
rs12676835	0.93[ASN][1000 genomes]
rs12677407	0.93[ASN][1000 genomes]
rs12678639	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12678680	0.88[AMR][1000 genomes]
rs12679287	0.93[ASN][1000 genomes]
rs12679983	0.87[ASN][1000 genomes]
rs12680128	0.87[ASN][1000 genomes]
rs12681203	0.93[ASN][1000 genomes]
rs12681734	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs13265006	0.96[ASN][1000 genomes]
rs13276400	0.91[ASN][1000 genomes]
rs16916820	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16916856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16916865	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16916906	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16916961	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17212214	0.93[ASN][1000 genomes]
rs17212256	0.93[ASN][1000 genomes]
rs17284746	0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs2037138	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2037139	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2069119	0.91[ASN][1000 genomes]
rs2176120	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34058697	0.94[ASN][1000 genomes]
rs34073804	0.89[ASN][1000 genomes]
rs34213209	0.91[ASN][1000 genomes]
rs34319820	0.89[ASN][1000 genomes]
rs34364864	0.99[ASN][1000 genomes]
rs34372756	0.93[ASN][1000 genomes]
rs34677273	0.93[ASN][1000 genomes]
rs34973406	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35032384	0.93[ASN][1000 genomes]
rs35509250	0.91[ASN][1000 genomes]
rs35603537	0.91[ASN][1000 genomes]
rs4292674	0.87[ASN][1000 genomes]
rs4321994	0.88[ASN][1000 genomes]
rs4534123	0.87[ASN][1000 genomes]
rs4598243	0.95[ASN][1000 genomes]
rs4626585	0.87[ASN][1000 genomes]
rs57212480	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58561048	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58583070	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59602923	0.93[ASN][1000 genomes]
rs60153173	0.89[ASN][1000 genomes]
rs60304457	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60796336	0.93[ASN][1000 genomes]
rs61326367	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6768	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs6994203	1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs71513549	0.87[ASN][1000 genomes]
rs71513552	0.89[ASN][1000 genomes]
rs71513561	0.96[ASN][1000 genomes]
rs71513564	0.93[ASN][1000 genomes]
rs763550	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9650179	0.93[ASN][1000 genomes]
rs9650180	0.93[ASN][1000 genomes]
rs9650305	0.93[ASN][1000 genomes]
rs9792352	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv967589	chr8:52731031-52735145	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41453644	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52717600-52735200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr8:52717600-52741800	Weak transcription	Aorta	Aorta
3	chr8:52717800-52734600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr8:52718000-52734800	Weak transcription	Dnd41	blood
5	chr8:52719400-52741800	Weak transcription	Esophagus	oesophagus
6	chr8:52719800-52734000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr8:52719800-52734600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr8:52720000-52735000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr8:52720800-52735000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr8:52720800-52737000	Weak transcription	Brain Anterior Caudate	brain
11	chr8:52721000-52741000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr8:52722000-52771400	Weak transcription	Gastric	stomach
13	chr8:52722200-52733600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr8:52722200-52733600	Weak transcription	Left Ventricle	heart
15	chr8:52722200-52734800	Weak transcription	Lung	lung
16	chr8:52722200-52752000	Weak transcription	Pancreas	Pancrea
17	chr8:52722400-52735000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr8:52722400-52741800	Weak transcription	Right Ventricle	heart
19	chr8:52722600-52734600	Weak transcription	Fetal Kidney	kidney
20	chr8:52722600-52735000	Weak transcription	HSMM	muscle
21	chr8:52722800-52733600	Weak transcription	Fetal Stomach	stomach
22	chr8:52722800-52733600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr8:52722800-52735200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr8:52722800-52735200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr8:52722800-52741000	Weak transcription	Colon Smooth Muscle	Colon
26	chr8:52722800-52741800	Weak transcription	HSMMtube	muscle
27	chr8:52723000-52741600	Weak transcription	Fetal Heart	heart
28	chr8:52726000-52735000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr8:52726000-52741800	Weak transcription	Brain Substantia Nigra	brain
30	chr8:52726800-52734600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr8:52727600-52756800	Weak transcription	Brain Angular Gyrus	brain
32	chr8:52728000-52734400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr8:52728200-52759200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr8:52728400-52734400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr8:52729800-52735000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr8:52729800-52741600	Weak transcription	Brain Hippocampus Middle	brain
37	chr8:52730000-52734600	Weak transcription	Adipose Nuclei	Adipose
38	chr8:52730400-52734800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr8:52731200-52734800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr8:52731200-52735200	Weak transcription	Spleen	Spleen
41	chr8:52731200-52763400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr8:52731200-52771000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr8:52731400-52733800	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr8:52731400-52753400	Weak transcription	NHDF-Ad	bronchial
45	chr8:52731600-52733800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr8:52731800-52733600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr8:52731800-52741800	Weak transcription	Psoas Muscle	Psoas
48	chr8:52731800-52745600	Weak transcription	NHEK	skin
49	chr8:52732000-52734000	Weak transcription	Fetal Lung	lung
50	chr8:52732200-52733600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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