Variant report

Variant	rs13430237
Chromosome Location	chr2:97558926-97558927
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:97557941..97560811-chr2:97624763..97627667,2	MCF-7	breast:
2	chr2:97556985..97558977-chr2:97588786..97591585,2	K562	blood:
3	chr2:97497342..97499040-chr2:97557166..97559196,2	MCF-7	breast:
4	chr2:97545881..97548014-chr2:97558703..97560346,2	K562	blood:
5	chr2:97530555..97533487-chr2:97558228..97559890,3	K562	blood:
6	chr2:97490386..97492773-chr2:97557628..97559451,2	MCF-7	breast:
7	chr2:97558219..97561795-chr2:97617145..97620359,3	K562	blood:
8	chr2:97530555..97532219-chr2:97558372..97559890,2	K562	blood:
9	chr2:97557540..97561219-chr2:97615825..97618671,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168758	Chromatin interaction
ENSG00000168763	Chromatin interaction
ENSG00000168754	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11902657	0.85[AFR][1000 genomes]
rs12464868	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12473528	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2314652	0.91[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2314653	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4243786	1.00[ASW][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4907254	1.00[ASW][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57632006	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6750988	0.85[ASN][1000 genomes]
rs72942920	0.82[AFR][1000 genomes]
rs7581764	0.86[MEX][hapmap]
rs7583821	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13430237	TXNDC9	cis	cerebellum	SCAN
rs13430237	NEURL3	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97552600-97560800	Weak transcription	Hela-S3	cervix
2	chr2:97554200-97560800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:97554400-97561000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:97554400-97563400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:97554600-97563400	Weak transcription	Fetal Heart	heart
6	chr2:97554800-97559200	Weak transcription	NHEK	skin
7	chr2:97554800-97561200	Weak transcription	Fetal Brain Female	brain
8	chr2:97555000-97560800	Weak transcription	Fetal Brain Male	brain
9	chr2:97555000-97561200	Weak transcription	Pancreas	Pancrea
10	chr2:97555600-97559800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:97555800-97559800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr2:97556000-97559000	Enhancers	Colon Smooth Muscle	Colon
13	chr2:97556000-97559400	Enhancers	Lung	lung
14	chr2:97556000-97560000	Transcr. at gene 5' and 3'	K562	blood
15	chr2:97556000-97560200	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr2:97556000-97560200	Enhancers	Brain Hippocampus Middle	brain
17	chr2:97556000-97562200	Enhancers	Brain Anterior Caudate	brain
18	chr2:97556200-97559200	Enhancers	Adipose Nuclei	Adipose
19	chr2:97556200-97559600	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr2:97556200-97559800	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr2:97556200-97560000	Enhancers	Primary T cells fromperipheralblood	blood
22	chr2:97556200-97560000	Enhancers	Psoas Muscle	Psoas
23	chr2:97556200-97560200	Enhancers	Primary T cells from cord blood	blood
24	chr2:97556200-97560200	Enhancers	Brain Angular Gyrus	brain
25	chr2:97556200-97560200	Enhancers	Brain Substantia Nigra	brain
26	chr2:97556200-97562200	Enhancers	Brain Cingulate Gyrus	brain
27	chr2:97556200-97562400	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr2:97556400-97559400	Enhancers	Spleen	Spleen
29	chr2:97556400-97559800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:97556400-97560200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:97556400-97565200	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr2:97556600-97559000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr2:97556600-97559400	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr2:97556600-97566000	Enhancers	Fetal Thymus	thymus
35	chr2:97556800-97562600	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr2:97557000-97561000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr2:97557200-97560000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr2:97557200-97561200	Weak transcription	Thymus	Thymus
39	chr2:97557400-97560800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr2:97557400-97560800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr2:97557400-97561000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr2:97557400-97561000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:97557600-97560800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:97557600-97561000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr2:97557600-97561000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr2:97557600-97561200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr2:97557600-97561200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:97557800-97560200	Enhancers	Placenta	Placenta
49	chr2:97557800-97560800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr2:97557800-97560800	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links