Variant report

Variant	rs4823086
Chromosome Location	chr22:30688659-30688660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30640449..30642621-chr22:30686801..30689268,2	MCF-7	breast:
2	chr22:30681129..30691076-chr22:30751303..30759078,14	K562	blood:
3	chr22:30686966..30689446-chr22:30691797..30694765,3	K562	blood:
4	chr22:30685533..30687274-chr22:30688307..30690442,2	K562	blood:

Variant related genes	Relation type
ENSG00000099992	Chromatin interaction
ENSG00000239282	Chromatin interaction
ENSG00000099995	Chromatin interaction
ENSG00000268812	Chromatin interaction
ENSG00000248751	Chromatin interaction
ENSG00000187860	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13056562	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13058084	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13058399	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13058535	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17730748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17738020	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[ASN][1000 genomes]
rs34102711	1.00[ASN][1000 genomes]
rs34318316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34911581	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34964064	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35074129	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35246430	1.00[ASN][1000 genomes]
rs35617977	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35960997	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4449240	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4820002	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820834	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823087	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67401267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73168654	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914968	chr22:30610570-30693581	Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv914969	chr22:30619599-30691631	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv834174	chr22:30619760-30746915	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv914971	chr22:30640308-30691631	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv914972	chr22:30640308-30693581	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1062388	chr22:30649179-30711443	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	esv1799458	chr22:30659798-30698035	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv588885	chr22:30661184-30691631	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv522605	chr22:30685076-30691631	Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4823086	RP1-130H16.16	cis	Thyroid	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30686000-30700000	Weak transcription	Fetal Kidney	kidney
2	chr22:30686200-30688800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr22:30686200-30689400	Weak transcription	Small Intestine	intestine
4	chr22:30686200-30691600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr22:30686200-30720000	Weak transcription	Fetal Brain Male	brain
6	chr22:30686400-30701800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr22:30686600-30700600	Genic enhancers	Fetal Thymus	thymus
8	chr22:30686800-30690400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr22:30686800-30694800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr22:30686800-30701800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr22:30686800-30707200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr22:30687000-30689000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr22:30687000-30695800	Strong transcription	Brain Germinal Matrix	brain
14	chr22:30687000-30699600	Strong transcription	Fetal Brain Female	brain
15	chr22:30687200-30689000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr22:30687200-30689000	Weak transcription	A549	lung
17	chr22:30687200-30689400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr22:30687200-30689600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr22:30687200-30697200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr22:30687400-30688800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr22:30687400-30689000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr22:30687400-30691600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr22:30687400-30692000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr22:30687400-30695200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr22:30687400-30695800	Strong transcription	Primary B cells from cord blood	blood
26	chr22:30687400-30696400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr22:30687400-30696600	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr22:30687400-30701200	Weak transcription	K562	blood
29	chr22:30687400-30706800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr22:30687600-30689400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr22:30687600-30689600	Genic enhancers	Fetal Muscle Trunk	muscle
32	chr22:30687600-30689600	Strong transcription	Thymus	Thymus
33	chr22:30687600-30689800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr22:30687600-30691000	Strong transcription	Primary T cells from cord blood	blood
35	chr22:30687600-30691000	Genic enhancers	Spleen	Spleen
36	chr22:30687600-30691200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr22:30687600-30691600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr22:30687600-30693000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr22:30687600-30693400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr22:30687600-30694000	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr22:30687600-30694200	Strong transcription	Fetal Intestine Large	intestine
42	chr22:30687600-30694600	Strong transcription	Fetal Intestine Small	intestine
43	chr22:30687600-30695600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr22:30687600-30696400	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr22:30687600-30697200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr22:30687600-30699000	Weak transcription	HepG2	liver
47	chr22:30687600-30699800	Genic enhancers	Esophagus	oesophagus
48	chr22:30687600-30701400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr22:30687800-30688800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
50	chr22:30687800-30689600	Weak transcription	Brain Hippocampus Middle	brain

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