Variant report

Variant	rs4926386
Chromosome Location	chr1:149886135-149886136
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:149884655..149886834-chr1:150138029..150140460,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10494260	0.92[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap]
rs11205309	0.86[JPT][hapmap]
rs11205310	0.86[JPT][hapmap]
rs12022928	0.86[JPT][hapmap]
rs12023231	0.92[GIH][hapmap];0.86[JPT][hapmap]
rs12409885	0.92[GIH][hapmap];0.86[JPT][hapmap]
rs17581597	1.00[MEX][hapmap]
rs1868992	0.83[GIH][hapmap]
rs3738320	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs3767627	0.92[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap]
rs3767628	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs3936952	0.84[GIH][hapmap];0.81[JPT][hapmap]
rs4926400	0.92[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap]
rs7551741	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432820	chr1:148921404-149920927	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	784 gene(s)	inside rSNPs	diseases
2	nsv831537	chr1:149833357-150064655	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	431 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4926386	TCHHL1	cis	parietal	SCAN
rs4926386	VPS72	cis	parietal	SCAN
rs4926386	LYSMD1	cis	parietal	SCAN
rs4926386	VPS45	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:149871800-149887400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:149872000-149887400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:149872000-149887600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:149872000-149887600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:149872000-149887800	Weak transcription	HSMMtube	muscle
6	chr1:149872200-149887400	Weak transcription	Right Atrium	heart
7	chr1:149872200-149887600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:149872200-149887600	Weak transcription	NH-A	brain
9	chr1:149872200-149887800	Weak transcription	Placenta	Placenta
10	chr1:149872200-149888000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:149872200-149888200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:149872200-149888400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:149872200-149888400	Weak transcription	Esophagus	oesophagus
14	chr1:149872400-149887400	Weak transcription	Spleen	Spleen
15	chr1:149872400-149887600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:149872400-149888200	Weak transcription	Colon Smooth Muscle	Colon
17	chr1:149872400-149888400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:149872400-149888400	Weak transcription	Right Ventricle	heart
19	chr1:149872600-149887200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:149872600-149887200	Weak transcription	Fetal Kidney	kidney
21	chr1:149872600-149887400	Weak transcription	Fetal Lung	lung
22	chr1:149872600-149888200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:149875000-149886200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:149875200-149887400	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:149876200-149887600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:149876600-149887600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:149876600-149888400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:149878400-149888800	Weak transcription	Gastric	stomach
29	chr1:149878800-149887800	Weak transcription	Fetal Intestine Small	intestine
30	chr1:149879400-149888400	Weak transcription	Brain Substantia Nigra	brain
31	chr1:149879600-149887000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:149879800-149888400	Weak transcription	Osteobl	bone
33	chr1:149880800-149888600	Weak transcription	Ovary	ovary
34	chr1:149882200-149887400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:149883600-149887400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:149883600-149887600	Weak transcription	Aorta	Aorta
37	chr1:149883800-149887600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr1:149884000-149886800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:149884600-149887400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr1:149884600-149888200	Weak transcription	NHDF-Ad	bronchial
41	chr1:149885000-149887400	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:149885200-149886600	Weak transcription	Brain Angular Gyrus	brain
43	chr1:149885200-149886600	Strong transcription	Fetal Brain Female	brain
44	chr1:149885200-149886800	Weak transcription	Fetal Brain Male	brain
45	chr1:149885200-149887400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr1:149885200-149887400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:149885400-149887000	Weak transcription	Brain Anterior Caudate	brain
48	chr1:149885400-149887200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr1:149885400-149887400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:149885400-149887400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links