Variant report

Variant	rs2231398
Chromosome Location	chr22:29656389-29656390
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:29656005-29657346	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr22:29655929-29657289	GM12878	blood:	n/a	n/a
3	POLR2A	chr22:29654643-29657160	GM18951	blood:	n/a	n/a
4	POLR2A	chr22:29656072-29657381	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr22:29653602-29657482	GM12891	blood:	n/a	n/a
6	POLR2A	chr22:29656299-29657380	K562	blood:	n/a	n/a
7	POLR2A	chr22:29654956-29657341	GM12891	blood:	n/a	n/a
8	POLR2A	chr22:29652410-29657525	GM12878	blood:	n/a	n/a
9	POLR2A	chr22:29655952-29657365	GM12878	blood:	n/a	n/a
10	POLR2A	chr22:29656077-29657501	HepG2	liver:	n/a	n/a
11	POLR2A	chr22:29655477-29657200	NB4	blood:	n/a	n/a
12	POLR2A	chr22:29654568-29657383	GM19193	blood:	n/a	n/a
13	POLR2A	chr22:29655891-29657670	GM12891	blood:	n/a	n/a
14	POLR2A	chr22:29655611-29657263	PBDE	blood:	n/a	n/a
15	POLR2A	chr22:29656276-29656522	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr22:29654506-29660719	HepG2	liver:	n/a	n/a
17	NFATC1	chr22:29656002-29656423	GM12878	blood:	n/a	n/a
18	POLR2A	chr22:29653683-29657301	GM12878	blood:	n/a	n/a
19	POLR2A	chr22:29653526-29658915	K562	blood:	n/a	n/a
20	POLR2A	chr22:29656296-29656561	GM12892	blood:	n/a	n/a
21	POLR2A	chr22:29654807-29657395	HL-60	blood:	n/a	n/a
22	POLR2A	chr22:29653540-29657993	SK-N-MC	brain:	n/a	n/a
23	POLR2A	chr22:29653559-29657623	GM12892	blood:	n/a	n/a
24	POLR2A	chr22:29653486-29657933	GM12892	blood:	n/a	n/a
25	POLR2A	chr22:29654916-29657883	GM12892	blood:	n/a	n/a
26	POLR2A	chr22:29654633-29658394	K562	blood:	n/a	n/a
27	POLR2A	chr22:29656146-29656541	U87	brain:	n/a	n/a
28	POLR2A	chr22:29656337-29656482	MCF-7	breast:	n/a	n/a
29	POLR2A	chr22:29654992-29656526	GM19099	blood:	n/a	n/a
30	POLR2A	chr22:29655899-29657120	K562	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29638508..29640700-chr22:29653710..29656559,2	K562	blood:
2	chr22:29654217..29657445-chr22:29658284..29661902,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000237015	TF binding region
ENSG00000100263	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11702906	1.00[JPT][hapmap]
rs11704551	1.00[JPT][hapmap]
rs131184	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs131190	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs140064	0.93[ASN][1000 genomes]
rs140065	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[ASN][1000 genomes]
rs174760	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[ASN][1000 genomes]
rs174768	1.00[JPT][hapmap]
rs174772	1.00[JPT][hapmap]
rs1894414	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2518683	0.82[CHB][hapmap];0.92[YRI][hapmap]
rs2857460	0.93[ASN][1000 genomes]
rs4823033	1.00[JPT][hapmap]
rs5997460	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[ASN][1000 genomes]
rs8140836	1.00[JPT][hapmap]

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	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv1809952	chr22:29595349-29661434	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv829154	chr22:29617485-29724001	Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Active TSS 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
4	nsv834171	chr22:29626402-29829844	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29622400-29656600	Weak transcription	Colonic Mucosa	Colon
2	chr22:29629000-29659400	Weak transcription	Brain Anterior Caudate	brain
3	chr22:29639800-29656400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr22:29641600-29659800	Weak transcription	Ovary	ovary
5	chr22:29641600-29661800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr22:29641800-29657800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr22:29642000-29659600	Weak transcription	Colon Smooth Muscle	Colon
8	chr22:29642200-29659800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr22:29642600-29662400	Strong transcription	Fetal Intestine Small	intestine
10	chr22:29643600-29660400	Weak transcription	Fetal Kidney	kidney
11	chr22:29644600-29659800	Weak transcription	Brain Substantia Nigra	brain
12	chr22:29647400-29662000	Strong transcription	Fetal Stomach	stomach
13	chr22:29648400-29657400	Strong transcription	Fetal Intestine Large	intestine
14	chr22:29649000-29662400	Weak transcription	Fetal Brain Male	brain
15	chr22:29649800-29657400	Strong transcription	Fetal Brain Female	brain
16	chr22:29650200-29657200	Strong transcription	Brain Germinal Matrix	brain
17	chr22:29650200-29662600	Weak transcription	Stomach Mucosa	stomach
18	chr22:29650600-29659800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr22:29650600-29660000	Weak transcription	Primary T cells from cord blood	blood
20	chr22:29650600-29660200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr22:29650800-29659800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr22:29651000-29659600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr22:29651000-29660000	Weak transcription	HepG2	liver
24	chr22:29651800-29659600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr22:29652200-29659800	Weak transcription	HMEC	breast
26	chr22:29652400-29660200	Weak transcription	NHEK	skin
27	chr22:29653400-29657800	Strong transcription	Fetal Muscle Leg	muscle
28	chr22:29653400-29658800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr22:29653400-29659800	Weak transcription	NHLF	lung
30	chr22:29653600-29656600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr22:29653600-29659600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr22:29653600-29662200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr22:29653800-29657400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr22:29653800-29657400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr22:29653800-29657400	Strong transcription	Fetal Muscle Trunk	muscle
36	chr22:29654000-29657800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr22:29654000-29659600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr22:29654000-29659800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr22:29654200-29656600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr22:29654200-29657400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr22:29654200-29657400	Strong transcription	Placenta	Placenta
42	chr22:29654200-29657400	Strong transcription	Stomach Smooth Muscle	stomach
43	chr22:29654200-29662600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr22:29654400-29656400	Weak transcription	HSMMtube	muscle
45	chr22:29654400-29656600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr22:29654400-29657600	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr22:29654400-29659800	Weak transcription	Aorta	Aorta
48	chr22:29654400-29660000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr22:29654600-29657200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr22:29654600-29657200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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