Variant report

Variant	rs12157641
Chromosome Location	chr22:31481922-31481923
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:31480215-31482031	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr22:31481864-31481959	K562	blood:	n/a	n/a
3	POLR2A	chr22:31480621-31481941	GM12878	blood:	n/a	n/a
4	POLR2A	chr22:31479356-31482395	GM12878	blood:	n/a	n/a
5	POLR2A	chr22:31481691-31482110	GM12878	blood:	n/a	n/a
6	POLR2A	chr22:31478535-31482422	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr22:31480061-31481938	HCT-116	colon:	n/a	n/a
8	POLR2A	chr22:31479922-31482025	K562	blood:	n/a	n/a
9	POLR2A	chr22:31478954-31482015	GM12892	blood:	n/a	n/a
10	POLR2A	chr22:31479046-31482278	GM12878	blood:	n/a	n/a
11	CTCF	chr22:31480072-31482631	SK-N-SH	brain:	n/a	chr22:31481340-31481350 chr22:31480917-31480930 chr22:31481338-31481354 chr22:31481339-31481352
12	POLR2A	chr22:31481885-31482301	ECC-1	luminal epithelium:	n/a	n/a
13	MXI1	chr22:31479991-31482030	SK-N-SH	brain:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:31476077..31485695-chr22:31490616..31506508,29	K562	blood:
2	chr22:31360911..31371148-chr22:31475052..31483145,24	K562	blood:
3	chr22:31360045..31368675-chr22:31475412..31482694,29	K562	blood:
4	chr22:31479621..31482894-chr22:31624206..31627128,3	K562	blood:
5	chr22:31455769..31462183-chr22:31475245..31482356,13	K562	blood:
6	chr22:31342107..31344742-chr22:31481093..31483316,2	K562	blood:
7	chr22:31354949..31372607-chr22:31475365..31485377,53	MCF-7	breast:
8	chr22:31458274..31462644-chr22:31476246..31482425,10	K562	blood:
9	chr22:31358868..31372302-chr22:31474097..31485545,64	MCF-7	breast:
10	chr22:31479652..31482728-chr22:31500685..31503831,4	MCF-7	breast:
11	chr22:31478816..31484481-chr22:31493390..31497944,7	MCF-7	breast:
12	chr22:31336067..31338299-chr22:31480944..31483823,2	MCF-7	breast:

No data

Variant related genes	Relation type
SMTN	TF binding region
ENSG00000273387	TF binding region
ENSG00000198832	Chromatin interaction
ENSG00000202019	Chromatin interaction
ENSG00000240186	Chromatin interaction
ENSG00000253352	Chromatin interaction
ENSG00000183963	Chromatin interaction
ENSG00000133422	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12165471	0.88[EUR][1000 genomes]
rs12330058	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs13053618	0.80[EUR][1000 genomes]
rs2074736	0.91[JPT][hapmap]
rs2074737	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2074738	0.96[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs35060453	0.88[EUR][1000 genomes]
rs5753433	0.81[CHB][hapmap]
rs5753456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5994368	0.81[EUR][1000 genomes]
rs5994370	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs5997871	0.87[EUR][1000 genomes]
rs8140524	0.83[JPT][hapmap]
rs9621175	0.87[EUR][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	nsv9896	chr22:31369204-31513933	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv829173	chr22:31450043-31543956	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv914975	chr22:31466083-31514477	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv914976	chr22:31475307-31543260	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv914977	chr22:31477563-31514477	Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31477800-31482000	Flanking Active TSS	NH-A	brain
2	chr22:31478000-31482200	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
3	chr22:31478200-31483400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr22:31478400-31484000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr22:31478400-31484000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr22:31478600-31483200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr22:31478800-31482600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr22:31479800-31482000	Enhancers	Fetal Brain Male	brain
9	chr22:31480600-31482000	Active TSS	Colon Smooth Muscle	Colon
10	chr22:31481000-31482000	Flanking Active TSS	Colonic Mucosa	Colon
11	chr22:31481000-31482000	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr22:31481000-31482400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr22:31481000-31484800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr22:31481200-31482000	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr22:31481200-31482000	Flanking Active TSS	Right Ventricle	heart
16	chr22:31481200-31482600	Enhancers	Fetal Heart	heart
17	chr22:31481400-31482000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
18	chr22:31481400-31482000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr22:31481400-31482000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr22:31481400-31482000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr22:31481400-31482000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr22:31481400-31482000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr22:31481400-31482000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
24	chr22:31481400-31482200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr22:31481400-31482200	Flanking Active TSS	Brain Hippocampus Middle	brain
26	chr22:31481400-31482600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr22:31481400-31494200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr22:31481400-31494600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr22:31481600-31482000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr22:31481600-31482000	Enhancers	Primary B cells from cord blood	blood
31	chr22:31481600-31482000	Enhancers	Primary T cells fromperipheralblood	blood
32	chr22:31481600-31482000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr22:31481600-31482000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr22:31481600-31482000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr22:31481600-31482000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr22:31481600-31482000	Flanking Active TSS	Brain Cingulate Gyrus	brain
37	chr22:31481600-31482000	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr22:31481600-31482000	Weak transcription	Left Ventricle	heart
39	chr22:31481600-31482000	Enhancers	Stomach Mucosa	stomach
40	chr22:31481600-31482000	Flanking Active TSS	Hela-S3	cervix
41	chr22:31481600-31482000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr22:31481600-31482200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr22:31481600-31482200	Enhancers	Primary B cells from peripheral blood	blood
44	chr22:31481600-31482200	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr22:31481600-31482200	Enhancers	Liver	Liver
46	chr22:31481600-31482200	Enhancers	Esophagus	oesophagus
47	chr22:31481600-31482200	Enhancers	Fetal Thymus	thymus
48	chr22:31481600-31482200	Enhancers	Lung	lung
49	chr22:31481600-31482200	Enhancers	Pancreas	Pancrea
50	chr22:31481600-31482200	Enhancers	Spleen	Spleen

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