Variant report

Variant	rs28730723
Chromosome Location	chr1:151144057-151144058
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151136854..151140829-chr1:151140868..151144448,5	K562	blood:
2	chr1:151040466..151042934-chr1:151142330..151145207,2	K562	blood:
3	chr1:150973043..150975367-chr1:151142300..151144414,2	MCF-7	breast:
4	chr1:151142755..151144595-chr1:151209312..151211204,2	MCF-7	breast:
5	chr1:151136705..151140829-chr1:151140868..151144071,4	K562	blood:

Variant related genes	Relation type
ENSG00000197622	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000163155	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11204787	0.88[CEU][hapmap];1.00[TSI][hapmap]
rs2305815	1.00[AFR][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	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs28730723	SELENBP1	cis	cerebellum	SCAN
rs28730723	MLLT11	cis	parietal	SCAN
rs28730723	LCE5A	cis	parietal	SCAN
rs28730723	PSMD4	cis	cerebellum	SCAN
rs28730723	CTSK	cis	cerebellum	SCAN
rs28730723	SELENBP1	cis	parietal	SCAN
rs28730723	PGLYRP3	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151139600-151144800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:151139600-151145800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:151139600-151147000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr1:151139600-151148400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:151139600-151149800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:151139600-151158600	Strong transcription	Fetal Stomach	stomach
7	chr1:151139600-151158600	Strong transcription	Lung	lung
8	chr1:151139600-151161600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:151139800-151144200	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:151139800-151144200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:151139800-151144200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:151139800-151144400	Strong transcription	Primary T cells from cord blood	blood
13	chr1:151139800-151146800	Weak transcription	Fetal Brain Male	brain
14	chr1:151139800-151147000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:151139800-151148200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:151139800-151149000	Weak transcription	Small Intestine	intestine
17	chr1:151139800-151158600	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:151139800-151158600	Strong transcription	Fetal Intestine Small	intestine
19	chr1:151139800-151159000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:151139800-151159400	Strong transcription	Fetal Brain Female	brain
21	chr1:151140000-151144200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:151140000-151144200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:151140000-151144200	Strong transcription	Liver	Liver
24	chr1:151140000-151144200	Strong transcription	Brain Hippocampus Middle	brain
25	chr1:151140000-151144200	Strong transcription	Dnd41	blood
26	chr1:151140000-151144400	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:151140000-151144600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr1:151140000-151145200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:151140000-151145800	Weak transcription	GM12878-XiMat	blood
30	chr1:151140000-151146200	Strong transcription	Fetal Muscle Trunk	muscle
31	chr1:151140000-151146800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:151140000-151146800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr1:151140000-151146800	Weak transcription	NH-A	brain
34	chr1:151140000-151147200	Strong transcription	Brain Germinal Matrix	brain
35	chr1:151140000-151149400	Weak transcription	K562	blood
36	chr1:151140000-151153400	Strong transcription	Placenta	Placenta
37	chr1:151140000-151158600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:151140000-151158600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:151140000-151158600	Strong transcription	Duodenum Mucosa	Duodenum
40	chr1:151140000-151158600	Strong transcription	Fetal Intestine Large	intestine
41	chr1:151140000-151158600	Strong transcription	Fetal Thymus	thymus
42	chr1:151140000-151158600	Strong transcription	Spleen	Spleen
43	chr1:151140000-151158800	Strong transcription	Primary B cells from peripheral blood	blood
44	chr1:151140000-151158800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:151140000-151159200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:151140000-151159200	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr1:151140000-151160000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:151140000-151160800	Weak transcription	Stomach Mucosa	stomach
49	chr1:151140200-151144200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:151140200-151144200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links