Variant report

Variant	rs11688998
Chromosome Location	chr2:39607976-39607977
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr2:39606873-39608311	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr2:39607851-39608248	MCF10A-Er-Src	breast:	n/a	n/a
3	TCF12	chr2:39607793-39608559	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr2:39607744-39608247	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr2:39607915-39608267	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr2:39607969-39608329	HepG2	liver:	n/a	n/a
7	FOS	chr2:39607839-39608315	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr2:39607971-39608290	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr2:39607928-39608176	MCF10A-Er-Src	breast:	n/a	n/a
10	MYC	chr2:39607954-39608368	MCF10A-Er-Src	breast:	n/a	n/a
11	GATA3	chr2:39607733-39608476	SK-N-SH	brain:	n/a	n/a
12	CTCF	chr2:39606100-39608053	A549	lung:	n/a	chr2:39606994-39607015 chr2:39606992-39607010
13	FOS	chr2:39607808-39608218	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:39603738..39609073-chr2:39660426..39665645,8	MCF-7	breast:
2	chr2:39592431..39595037-chr2:39606994..39609633,2	MCF-7	breast:
3	chr2:39594087..39595987-chr2:39607916..39609547,2	MCF-7	breast:
4	chr2:39605627..39608331-chr2:39913842..39916545,2	MCF-7	breast:
5	chr2:39601552..39609752-chr2:39662569..39667062,10	MCF-7	breast:

Variant related genes	Relation type
MAP4K3	TF binding region
ENSG00000011566	Chromatin interaction
ENSG00000152154	Chromatin interaction
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10196253	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11124681	0.94[ASN][1000 genomes]
rs17023504	0.94[ASN][1000 genomes]
rs17023656	1.00[ASN][1000 genomes]
rs17023777	1.00[ASN][1000 genomes]
rs3755175	0.94[ASN][1000 genomes]
rs3770676	0.94[ASN][1000 genomes]
rs3770677	0.94[ASN][1000 genomes]
rs3770679	0.94[ASN][1000 genomes]
rs55748017	0.94[ASN][1000 genomes]
rs56833014	1.00[ASN][1000 genomes]
rs57103739	0.94[ASN][1000 genomes]
rs57232122	0.88[ASN][1000 genomes]
rs58704884	1.00[ASN][1000 genomes]
rs60192971	1.00[ASN][1000 genomes]
rs61480659	1.00[ASN][1000 genomes]
rs6544226	0.94[ASN][1000 genomes]
rs7591102	0.83[ASN][1000 genomes]

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	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39587000-39608800	Weak transcription	Pancreas	Pancrea
2	chr2:39588000-39608800	Weak transcription	Lung	lung
3	chr2:39588000-39609000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:39588000-39630400	Weak transcription	Placenta	Placenta
5	chr2:39591800-39621400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:39592800-39617600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:39594600-39608800	Weak transcription	Left Ventricle	heart
8	chr2:39600600-39614600	Weak transcription	Aorta	Aorta
9	chr2:39601600-39609000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:39603200-39608200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:39603200-39609000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:39603200-39638400	Weak transcription	Hela-S3	cervix
13	chr2:39603400-39612000	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:39603400-39613200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:39603400-39625000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:39603400-39626800	Weak transcription	Primary T cells from cord blood	blood
17	chr2:39604400-39610200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:39604600-39609600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr2:39604600-39610400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:39604600-39610800	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr2:39604800-39609200	Enhancers	HSMMtube	muscle
22	chr2:39605000-39608800	Weak transcription	Psoas Muscle	Psoas
23	chr2:39605000-39609000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:39605000-39609000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:39605000-39609000	Weak transcription	Right Atrium	heart
26	chr2:39605000-39609600	Enhancers	Rectal Smooth Muscle	rectum
27	chr2:39605000-39609800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:39605200-39609000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:39605200-39609000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr2:39605200-39609200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr2:39605400-39609400	Enhancers	HSMM	muscle
32	chr2:39605600-39608400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr2:39605600-39609600	Enhancers	Brain Hippocampus Middle	brain
34	chr2:39605600-39612400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:39605800-39608400	Enhancers	Adipose Nuclei	Adipose
36	chr2:39605800-39612200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:39606200-39608400	Enhancers	Brain Angular Gyrus	brain
38	chr2:39606200-39608400	Enhancers	Brain Substantia Nigra	brain
39	chr2:39606200-39609000	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr2:39606200-39609200	Enhancers	Liver	Liver
41	chr2:39606200-39609400	Enhancers	Brain Anterior Caudate	brain
42	chr2:39606200-39609600	Enhancers	Osteobl	bone
43	chr2:39606200-39610400	Enhancers	Fetal Heart	heart
44	chr2:39606400-39609400	Enhancers	Brain Cingulate Gyrus	brain
45	chr2:39606400-39610000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:39606400-39610000	Enhancers	Colon Smooth Muscle	Colon
47	chr2:39606400-39614000	Weak transcription	Right Ventricle	heart
48	chr2:39606600-39608000	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr2:39606600-39608400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:39606600-39609200	Enhancers	NHDF-Ad	bronchial

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