Variant report

Variant	rs13002561
Chromosome Location	chr2:9909640-9909641
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9895791..9898200-chr2:9907765..9909723,2	MCF-7	breast:
2	chr2:9694937..9699400-chr2:9908606..9911252,4	K562	blood:
3	chr2:9909026..9912481-chr2:10259443..10262566,4	K562	blood:
4	chr2:9909277..9910874-chr2:10183510..10185614,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271855	Chromatin interaction
ENSG00000171848	Chromatin interaction
ENSG00000172059	Chromatin interaction
ENSG00000151694	Chromatin interaction
ENSG00000272524	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11675210	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11676697	0.84[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11676974	1.00[JPT][hapmap]
rs11677860	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11691911	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11693428	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11693486	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12987514	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12998168	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs870119	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs870120	0.91[CEU][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469405	chr2:9814374-9964947	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv580930	chr2:9814374-9964947	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv470443	chr2:9857018-9975557	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv873618	chr2:9870631-9919759	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv873619	chr2:9870631-9956981	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1013969	chr2:9888703-10023951	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv873620	chr2:9906145-9951970	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13002561	DEF8	cis	Cerebellum	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9901800-9910200	Weak transcription	Brain Hippocampus Middle	brain
2	chr2:9903000-9911800	Enhancers	Fetal Intestine Small	intestine
3	chr2:9903200-9912000	Enhancers	Fetal Intestine Large	intestine
4	chr2:9903600-9910400	Weak transcription	Psoas Muscle	Psoas
5	chr2:9903600-9910800	Weak transcription	Left Ventricle	heart
6	chr2:9904200-9910000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:9904800-9910400	Weak transcription	Colon Smooth Muscle	Colon
8	chr2:9904800-9910400	Weak transcription	Hela-S3	cervix
9	chr2:9905000-9910000	Weak transcription	Fetal Kidney	kidney
10	chr2:9905000-9910200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:9905200-9913000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr2:9905600-9909800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:9906200-9912000	Enhancers	Fetal Thymus	thymus
14	chr2:9906400-9909800	Enhancers	Primary B cells from cord blood	blood
15	chr2:9906400-9910600	Weak transcription	Small Intestine	intestine
16	chr2:9906800-9909800	Weak transcription	Placenta	Placenta
17	chr2:9906800-9910400	Weak transcription	Lung	lung
18	chr2:9906800-9910400	Weak transcription	Right Atrium	heart
19	chr2:9906800-9910400	Weak transcription	Right Ventricle	heart
20	chr2:9906800-9910400	Weak transcription	A549	lung
21	chr2:9907200-9910200	Weak transcription	NHEK	skin
22	chr2:9907600-9911200	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr2:9907600-9913600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:9907800-9910000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:9907800-9910400	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr2:9907800-9911200	Enhancers	H1 Cell Line	embryonic stem cell
27	chr2:9907800-9912000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:9908000-9911000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:9908000-9911000	Enhancers	GM12878-XiMat	blood
30	chr2:9908000-9911200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:9908000-9911200	Enhancers	Pancreas	Pancrea
32	chr2:9908000-9911200	Enhancers	Spleen	Spleen
33	chr2:9908000-9912200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
34	chr2:9908000-9912400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:9908000-9912600	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr2:9908000-9915200	Enhancers	Fetal Muscle Leg	muscle
37	chr2:9908200-9909800	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr2:9908200-9910200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
39	chr2:9908200-9910600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
40	chr2:9908200-9911600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:9908200-9912200	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr2:9908200-9913600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:9908400-9910200	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr2:9908400-9910200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr2:9908400-9911200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:9908400-9911200	Enhancers	K562	blood
47	chr2:9908400-9912000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:9908400-9912000	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr2:9908400-9912400	Enhancers	Esophagus	oesophagus
50	chr2:9908600-9909800	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links