Variant report

Variant	rs1882494
Chromosome Location	chr12:104879777-104879778
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104876677..104879866-chr12:104887122..104889642,3	K562	blood:
2	chr12:104869578..104872458-chr12:104877687..104880614,4	K562	blood:
3	chr12:104878866..104881673-chr12:104885573..104889432,3	K562	blood:
4	chr12:104879669..104882101-chr12:104882975..104884643,2	K562	blood:
5	chr12:104871756..104873492-chr12:104876935..104879923,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11608669	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11609491	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17035663	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2141855	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2141856	0.89[ASN][1000 genomes]
rs4536299	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs55778791	0.85[ASN][1000 genomes]
rs56020814	0.89[ASN][1000 genomes]
rs56138293	1.00[ASN][1000 genomes]
rs60351248	0.89[ASN][1000 genomes]
rs7970489	0.85[ASN][1000 genomes]
rs7972097	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972201	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][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	nsv832502	chr12:104833729-104908288	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv868	chr12:104858964-104895572	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1042647	chr12:104861494-104888494	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1882494	PMCH	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104859200-104879800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr12:104866600-104882400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:104869200-104899600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:104872600-104882400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:104872800-104879800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr12:104872800-104880600	Weak transcription	Stomach Mucosa	stomach
7	chr12:104872800-104883000	Enhancers	Primary B cells from peripheral blood	blood
8	chr12:104872800-104887000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:104873000-104887600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr12:104873200-104895400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:104873800-104880800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:104874800-104880000	Weak transcription	Aorta	Aorta
13	chr12:104875000-104879800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr12:104875000-104880400	Weak transcription	Osteobl	bone
15	chr12:104875000-104887000	Weak transcription	Placenta	Placenta
16	chr12:104875200-104880200	Weak transcription	Fetal Stomach	stomach
17	chr12:104875200-104880600	Weak transcription	Adipose Nuclei	Adipose
18	chr12:104875200-104880800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:104875200-104882000	Weak transcription	Gastric	stomach
20	chr12:104875200-104882400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr12:104875200-104888000	Weak transcription	HMEC	breast
22	chr12:104875200-104895400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:104875200-104897000	Weak transcription	NHEK	skin
24	chr12:104875400-104879800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:104875400-104880200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr12:104875400-104880200	Weak transcription	HSMM	muscle
27	chr12:104875400-104880600	Weak transcription	Fetal Intestine Small	intestine
28	chr12:104875400-104904200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:104876800-104879800	Weak transcription	Brain Hippocampus Middle	brain
30	chr12:104876800-104880600	Weak transcription	A549	lung
31	chr12:104877000-104879800	Weak transcription	Small Intestine	intestine
32	chr12:104877000-104882000	Weak transcription	Fetal Lung	lung
33	chr12:104877400-104881600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:104877600-104879800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr12:104877800-104880200	Enhancers	Duodenum Mucosa	Duodenum
36	chr12:104877800-104887000	Enhancers	Primary T cells fromperipheralblood	blood
37	chr12:104878000-104885400	Enhancers	Primary hematopoietic stem cells	blood
38	chr12:104878000-104886000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:104878400-104882600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:104878600-104881200	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr12:104878600-104882200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr12:104878600-104885000	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr12:104878800-104880000	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr12:104878800-104880400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:104879000-104879800	Flanking Active TSS	Dnd41	blood
46	chr12:104879000-104880400	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr12:104879000-104880400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr12:104879200-104879800	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr12:104879200-104880000	Enhancers	H1 Cell Line	embryonic stem cell
50	chr12:104879200-104880000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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