Variant report

Variant	rs12544903
Chromosome Location	chr8:52786066-52786067
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:52785279..52786991-chr8:52811511..52813258,2	K562	blood:
2	chr8:52785415..52788968-chr8:52790350..52793500,3	K562	blood:
3	chr8:52780733..52786342-chr8:52810229..52813272,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228801	Chromatin interaction
ENSG00000168300	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11551686	1.00[ASN][1000 genomes]
rs11989650	0.81[EUR][1000 genomes]
rs12541846	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12543540	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12545812	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12545881	1.00[ASN][1000 genomes]
rs16916754	0.81[EUR][1000 genomes]
rs28451175	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4873202	0.81[EUR][1000 genomes]
rs56117807	0.97[ASN][1000 genomes]
rs6473644	0.81[EUR][1000 genomes]
rs6473665	1.00[ASN][1000 genomes]
rs6984728	0.81[EUR][1000 genomes]
rs6987025	0.91[EUR][1000 genomes]
rs6993171	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7015360	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73583651	1.00[ASN][1000 genomes]
rs73583663	0.93[ASN][1000 genomes]
rs7819631	1.00[ASN][1000 genomes]
rs9643465	1.00[ASN][1000 genomes]

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	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
5	nsv526922	chr8:52772515-52786791	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12544903	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52759000-52786200	Weak transcription	Lung	lung
2	chr8:52759200-52786200	Weak transcription	Spleen	Spleen
3	chr8:52764000-52793400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr8:52767400-52796600	Weak transcription	Fetal Brain Male	brain
5	chr8:52769800-52793600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr8:52771000-52797800	Weak transcription	Fetal Stomach	stomach
7	chr8:52771800-52786200	Weak transcription	Gastric	stomach
8	chr8:52771800-52797000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr8:52771800-52810800	Weak transcription	Esophagus	oesophagus
10	chr8:52772200-52807600	Weak transcription	HSMMtube	muscle
11	chr8:52772400-52793200	Weak transcription	Fetal Heart	heart
12	chr8:52773000-52791200	Weak transcription	Thymus	Thymus
13	chr8:52773000-52803200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr8:52773600-52797000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr8:52773600-52797200	Weak transcription	Placenta	Placenta
16	chr8:52775600-52786200	Weak transcription	Small Intestine	intestine
17	chr8:52779400-52796200	Weak transcription	Brain Germinal Matrix	brain
18	chr8:52779400-52809000	Weak transcription	Fetal Kidney	kidney
19	chr8:52780400-52786200	Weak transcription	Right Ventricle	heart
20	chr8:52780400-52796400	Weak transcription	Liver	Liver
21	chr8:52780800-52803200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr8:52781000-52791200	Weak transcription	Fetal Lung	lung
23	chr8:52781000-52793400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr8:52781200-52788200	Weak transcription	Colonic Mucosa	Colon
25	chr8:52781200-52790600	Weak transcription	Fetal Intestine Small	intestine
26	chr8:52782200-52809600	Weak transcription	Aorta	Aorta
27	chr8:52782800-52786200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr8:52782800-52786200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr8:52782800-52787800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr8:52782800-52791000	Weak transcription	Right Atrium	heart
31	chr8:52782800-52796200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr8:52783000-52786200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr8:52783000-52786200	Weak transcription	Dnd41	blood
34	chr8:52783000-52786400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr8:52783000-52791200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr8:52783000-52796800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr8:52783000-52797200	Weak transcription	HSMM	muscle
38	chr8:52783000-52803200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr8:52783000-52803400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr8:52783000-52803600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr8:52783200-52786400	Enhancers	Colon Smooth Muscle	Colon
42	chr8:52783200-52791000	Weak transcription	Adipose Nuclei	Adipose
43	chr8:52783200-52795800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr8:52783200-52796400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr8:52783200-52797200	Weak transcription	Fetal Brain Female	brain
46	chr8:52783400-52787000	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr8:52783400-52787600	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr8:52783400-52788800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr8:52783400-52796600	Weak transcription	NHEK	skin
50	chr8:52783400-52796800	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links