Variant report

Variant	rs4381823
Chromosome Location	chr2:48047335-48047336
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48045856..48048073-chr2:48050684..48052432,2	K562	blood:
2	chr2:48040148..48042621-chr2:48045364..48047851,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138081	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10490303	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10495948	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17036952	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17036971	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17037021	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17037040	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17037055	1.00[CEU][hapmap]
rs17037062	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17037064	1.00[CEU][hapmap]
rs2134055	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2881863	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3136242	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3136274	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3136286	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56682209	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56881113	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58057481	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58552166	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59624704	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60118201	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60303023	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6704872	0.88[GIH][hapmap]
rs72876814	1.00[EUR][1000 genomes]
rs7560678	0.85[AFR][1000 genomes];1.00[AMR][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	nsv998096	chr2:47939614-48131697	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription 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	36 gene(s)	inside rSNPs	diseases
3	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv930955	chr2:48040218-48121218	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Schizophrenia	23894747	GWAS catalog

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48012600-48065000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:48016200-48050400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr2:48017000-48049400	Strong transcription	Fetal Intestine Large	intestine
4	chr2:48017200-48053200	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:48017400-48049600	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr2:48021200-48051600	Strong transcription	Placenta	Placenta
7	chr2:48021400-48067600	Strong transcription	Dnd41	blood
8	chr2:48021600-48067000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:48022200-48050200	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr2:48022800-48049200	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr2:48022800-48050000	Strong transcription	HUVEC	blood vessel
12	chr2:48023200-48065000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:48030200-48067600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr2:48030400-48067000	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:48030800-48048000	Strong transcription	Hela-S3	cervix
16	chr2:48030800-48049400	Strong transcription	Fetal Muscle Trunk	muscle
17	chr2:48030800-48049600	Strong transcription	Duodenum Mucosa	Duodenum
18	chr2:48030800-48067000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:48030800-48067000	Strong transcription	Fetal Thymus	thymus
20	chr2:48031000-48049400	Strong transcription	Fetal Brain Female	brain
21	chr2:48031000-48053000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:48031000-48067000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr2:48031000-48067000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:48031000-48067200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:48031200-48048600	Strong transcription	K562	blood
26	chr2:48031200-48049600	Strong transcription	Primary B cells from cord blood	blood
27	chr2:48031200-48053800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:48031200-48065800	Strong transcription	Liver	Liver
29	chr2:48031200-48066800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:48031400-48050000	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:48031400-48051400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:48031400-48060600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:48031400-48066800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:48031400-48067000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:48031400-48067800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:48031400-48067800	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:48031400-48072600	Weak transcription	Stomach Mucosa	stomach
38	chr2:48032000-48058000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr2:48032200-48067000	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr2:48032400-48066800	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr2:48032400-48068400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:48033600-48067000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr2:48033800-48067400	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr2:48036000-48047400	Weak transcription	Small Intestine	intestine
45	chr2:48036000-48067800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr2:48036200-48047400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr2:48037600-48049400	Strong transcription	Fetal Muscle Leg	muscle
48	chr2:48038000-48061200	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr2:48038200-48051800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:48038200-48071400	Weak transcription	Fetal Heart	heart

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