Variant report

Variant	rs539324
Chromosome Location	chr1:179938305-179938306
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179921069..179927710-chr1:179937007..179944258,10	K562	blood:
2	chr1:179937946..179940776-chr1:179952862..179955374,2	K562	blood:

Variant related genes	Relation type
ENSG00000260360	Chromatin interaction
ENSG00000135837	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10913918	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1281384	0.83[ASN][1000 genomes]
rs1281386	0.83[ASN][1000 genomes]
rs1281389	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2281805	0.88[ASN][1000 genomes]
rs2319677	0.89[EUR][1000 genomes]
rs2477114	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2777910	0.81[ASN][1000 genomes]
rs2985373	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4147170	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4147171	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4622030	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs504202	0.85[ASN][1000 genomes]
rs511332	0.85[ASN][1000 genomes]
rs521858	0.85[ASN][1000 genomes]
rs526683	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs533795	0.83[ASN][1000 genomes]
rs551607	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs552743	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs561233	0.83[ASN][1000 genomes]
rs6425606	0.85[EUR][1000 genomes]
rs6425607	0.85[EUR][1000 genomes]
rs6682558	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7521895	0.91[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	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers 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	48 gene(s)	inside rSNPs	diseases
3	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv946526	chr1:179936327-179938655	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179924800-179963600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:179925200-179946200	Weak transcription	Stomach Mucosa	stomach
3	chr1:179925400-179946000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:179925600-179938400	Weak transcription	HSMM	muscle
5	chr1:179925800-179940600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:179926000-179938400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:179926800-179961400	Weak transcription	A549	lung
8	chr1:179927000-179965600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:179927200-179940600	Weak transcription	NHDF-Ad	bronchial
10	chr1:179928000-179939000	Weak transcription	Fetal Heart	heart
11	chr1:179934600-179939200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:179934600-179945000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:179935200-179938400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:179936000-179938400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:179936000-179946400	Weak transcription	NHLF	lung
16	chr1:179936200-179938400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:179936200-179938400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:179936200-179939200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:179936200-179946000	Weak transcription	Fetal Lung	lung
20	chr1:179936200-179946000	Weak transcription	HepG2	liver
21	chr1:179936400-179955600	Weak transcription	Dnd41	blood
22	chr1:179936600-179938600	Strong transcription	Fetal Stomach	stomach
23	chr1:179936600-179958800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:179936800-179938600	Strong transcription	Fetal Intestine Small	intestine
25	chr1:179937200-179938800	Weak transcription	GM12878-XiMat	blood
26	chr1:179937200-179941200	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr1:179937400-179941200	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr1:179937600-179938400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
29	chr1:179937600-179938400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:179937600-179938600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:179937600-179938600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:179937600-179938600	Genic enhancers	Primary T cells from cord blood	blood
33	chr1:179937600-179938600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:179937600-179938600	Enhancers	Ovary	ovary
35	chr1:179937600-179939200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:179937600-179939800	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr1:179937600-179939800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:179937600-179939800	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr1:179937600-179941400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:179937600-179941400	Enhancers	Brain Hippocampus Middle	brain
41	chr1:179937800-179938400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr1:179937800-179938400	Strong transcription	Fetal Muscle Trunk	muscle
43	chr1:179937800-179938600	Genic enhancers	Fetal Thymus	thymus
44	chr1:179937800-179938600	Genic enhancers	Stomach Smooth Muscle	stomach
45	chr1:179937800-179938600	Strong transcription	Thymus	Thymus
46	chr1:179937800-179938600	Enhancers	Spleen	Spleen
47	chr1:179937800-179938600	Enhancers	K562	blood
48	chr1:179937800-179938800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr1:179937800-179938800	Strong transcription	Fetal Intestine Large	intestine
50	chr1:179937800-179938800	Enhancers	Right Ventricle	heart

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