Variant report

Variant	rs55750780
Chromosome Location	chr2:39661809-39661810
allele	G/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	GATA1	chr2:39660629-39661905	PBDE	blood:	n/a	chr2:39660959-39660968 chr2:39660907-39660917 chr2:39661770-39661783 chr2:39661593-39661600
2	GATA2	chr2:39661473-39661893	SH-SY5Y	brain:	n/a	chr2:39661770-39661783 chr2:39661593-39661600
3	RCOR1	chr2:39661502-39661961	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:39661430..39663106-chr2:39773041..39775918,2	MCF-7	breast:
2	chr2:39603738..39609073-chr2:39660426..39665645,8	MCF-7	breast:
3	chr2:39655304..39658022-chr2:39658367..39662517,3	K562	blood:
4	chr2:39661305..39663930-chr2:39740460..39742003,2	MCF-7	breast:

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

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11886434	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11895366	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55961227	0.81[AFR][1000 genomes]
rs57084694	0.95[AFR][1000 genomes]
rs58824151	0.81[AFR][1000 genomes]
rs59896787	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60394429	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544225	0.81[AFR][1000 genomes]
rs6712399	0.82[AFR][1000 genomes]
rs6723987	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6727395	0.82[AFR][1000 genomes]
rs6751506	0.82[AFR][1000 genomes]
rs73923887	0.81[AFR][1000 genomes]
rs73923888	0.81[AFR][1000 genomes]
rs73923889	0.81[AFR][1000 genomes]
rs73924011	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73924013	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73924016	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7565210	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7591563	0.81[AFR][1000 genomes]
rs7599017	0.82[AFR][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	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
2	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
3	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
4	nsv2695	chr2:39643221-39688015	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39652000-39662400	Weak transcription	Esophagus	oesophagus
2	chr2:39652000-39662400	Weak transcription	Lung	lung
3	chr2:39656600-39662200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:39657800-39662400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr2:39658000-39662400	Enhancers	Liver	Liver
6	chr2:39658200-39662400	Enhancers	H1 Cell Line	embryonic stem cell
7	chr2:39658400-39662400	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr2:39658600-39662800	Enhancers	Stomach Mucosa	stomach
9	chr2:39658600-39663000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr2:39659000-39663000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:39659200-39662400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:39659200-39662600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:39659200-39663400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr2:39659400-39662400	Active TSS	GM12878-XiMat	blood
15	chr2:39659800-39662200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr2:39660000-39662200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:39660000-39663200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:39660000-39663400	Flanking Active TSS	K562	blood
19	chr2:39660200-39662000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:39660200-39662200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:39660200-39662200	Enhancers	Fetal Intestine Small	intestine
22	chr2:39660200-39662400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr2:39660200-39663200	Enhancers	Small Intestine	intestine
24	chr2:39660400-39662000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:39660400-39662200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:39660400-39662600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:39660600-39662200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr2:39660800-39662200	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr2:39660800-39662200	Enhancers	Brain Germinal Matrix	brain
30	chr2:39660800-39662200	Enhancers	Fetal Intestine Large	intestine
31	chr2:39660800-39662200	Enhancers	Fetal Muscle Leg	muscle
32	chr2:39660800-39662200	Enhancers	Placenta	Placenta
33	chr2:39660800-39662600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:39661000-39662000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:39661000-39662200	Enhancers	H9 Cell Line	embryonic stem cell
36	chr2:39661000-39662200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:39661000-39662200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:39661000-39663000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:39661000-39666000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:39661200-39662000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr2:39661200-39662200	Enhancers	Brain Anterior Caudate	brain
42	chr2:39661200-39662200	Enhancers	HUVEC	blood vessel
43	chr2:39661200-39662400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr2:39661200-39663000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:39661200-39663000	Flanking Active TSS	Fetal Heart	heart
46	chr2:39661200-39665000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:39661400-39662000	Flanking Active TSS	Ovary	ovary
48	chr2:39661400-39662000	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr2:39661400-39662000	Flanking Active TSS	NHLF	lung
50	chr2:39661400-39662200	Enhancers	Brain Angular Gyrus	brain

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