Variant report

Variant	rs4670936
Chromosome Location	chr2:39660054-39660055
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr2:39659750-39660556	HepG2	liver:	n/a	n/a
2	FOXA1	chr2:39659832-39660488	HepG2	liver:	n/a	n/a
3	FOXA2	chr2:39659851-39660130	HepG2	liver:	n/a	n/a
4	FOXA1	chr2:39659850-39660125	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:39657902..39660340-chr2:39663128..39665771,3	K562	blood:
2	chr2:39652432..39656926-chr2:39657241..39661273,4	MCF-7	breast:
3	chr2:39654384..39656809-chr2:39659803..39661309,2	MCF-7	breast:
4	chr2:39655304..39658022-chr2:39658367..39662517,3	K562	blood:
5	chr2:39654637..39656374-chr2:39657864..39660833,3	K562	blood:

No data

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

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10169391	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10170424	0.89[AFR][1000 genomes]
rs10170604	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10173556	0.84[AFR][1000 genomes]
rs10175333	0.90[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10181650	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1035232	0.84[AFR][1000 genomes]
rs10865150	0.83[YRI][hapmap]
rs10865152	0.84[AFR][1000 genomes]
rs11124676	0.90[YRI][hapmap]
rs11124679	0.88[AFR][1000 genomes]
rs11124681	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12614034	0.87[AFR][1000 genomes]
rs12622941	0.80[YRI][hapmap]
rs12712641	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13028561	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1474424	0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1477164	0.82[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1922827	0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs2005892	0.82[AFR][1000 genomes]
rs2056654	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2111382	1.00[AMR][1000 genomes]
rs2160661	1.00[AMR][1000 genomes]
rs2178762	0.86[AFR][1000 genomes]
rs2193422	0.84[AFR][1000 genomes]
rs2373534	0.81[YRI][hapmap]
rs2373536	0.90[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2708224	0.83[AMR][1000 genomes]
rs2888598	0.86[AFR][1000 genomes]
rs3755178	0.90[YRI][hapmap]
rs4670934	0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4670935	0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6419603	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544222	0.85[AFR][1000 genomes]
rs6544223	0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544228	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6717792	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6724393	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6730902	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6732611	0.91[AFR][1000 genomes]
rs6741312	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs6742170	0.84[AFR][1000 genomes]
rs6743041	0.90[YRI][hapmap]
rs6759495	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6760382	0.84[AFR][1000 genomes]
rs7578136	0.82[AFR][1000 genomes]
rs7582160	0.83[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7591102	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7595041	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7601700	0.83[YRI][hapmap]
rs7603392	0.90[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7608153	0.80[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:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39644200-39661600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:39646000-39660200	Weak transcription	Fetal Intestine Small	intestine
3	chr2:39647800-39660200	Weak transcription	Pancreas	Pancrea
4	chr2:39652000-39662400	Weak transcription	Esophagus	oesophagus
5	chr2:39652000-39662400	Weak transcription	Lung	lung
6	chr2:39652400-39661200	Weak transcription	HUVEC	blood vessel
7	chr2:39652800-39660200	Weak transcription	Ovary	ovary
8	chr2:39652800-39661400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:39652800-39661400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr2:39652800-39661600	Weak transcription	Fetal Thymus	thymus
11	chr2:39654400-39660400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:39655200-39660400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:39656600-39660600	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr2:39656600-39660800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:39656600-39661200	Enhancers	Fetal Heart	heart
16	chr2:39656600-39661800	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr2:39656600-39662200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:39657200-39661200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr2:39657400-39660800	Weak transcription	NH-A	brain
20	chr2:39657400-39661600	Enhancers	Adipose Nuclei	Adipose
21	chr2:39657600-39660600	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr2:39657600-39661200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:39657800-39660800	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr2:39657800-39661000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr2:39657800-39661600	Enhancers	NHDF-Ad	bronchial
26	chr2:39657800-39661800	Enhancers	Colon Smooth Muscle	Colon
27	chr2:39657800-39662400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr2:39658000-39660400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr2:39658000-39661400	Enhancers	HSMMtube	muscle
30	chr2:39658000-39661600	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr2:39658000-39661600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:39658000-39662400	Enhancers	Liver	Liver
33	chr2:39658200-39660200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:39658200-39660400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:39658200-39661200	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr2:39658200-39661600	Enhancers	Hela-S3	cervix
37	chr2:39658200-39662400	Enhancers	H1 Cell Line	embryonic stem cell
38	chr2:39658400-39661800	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr2:39658400-39662400	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr2:39658600-39660400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:39658600-39661000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:39658600-39662800	Enhancers	Stomach Mucosa	stomach
43	chr2:39658600-39663000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr2:39658800-39660200	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr2:39658800-39660600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:39658800-39660600	Weak transcription	Fetal Brain Male	brain
47	chr2:39658800-39660800	Weak transcription	Gastric	stomach
48	chr2:39659000-39660200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr2:39659000-39660200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr2:39659000-39660200	Enhancers	Primary T cells from cord blood	blood

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