Variant report

Variant	rs4670273
Chromosome Location	chr2:39660377-39660378
allele	C/G
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	IRF1	chr2:39660342-39660542	K562	blood:	n/a	n/a
2	FOXA1	chr2:39659750-39660556	HepG2	liver:	n/a	n/a
3	FOXA1	chr2:39659832-39660488	HepG2	liver:	n/a	n/a

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

Variant related genes	Relation type
ENSG00000231312	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10169501	0.81[ASN][1000 genomes]
rs10173722	0.80[ASN][1000 genomes]
rs10196447	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs10199459	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10199948	0.81[JPT][hapmap]
rs11124683	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11896389	0.91[EUR][1000 genomes]
rs12328714	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17023530	0.94[EUR][1000 genomes]
rs17023542	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs17023547	0.85[CEU][hapmap];0.94[EUR][1000 genomes]
rs17023600	0.94[EUR][1000 genomes]
rs17023611	0.94[EUR][1000 genomes]
rs17023684	1.00[EUR][1000 genomes]
rs17023696	0.82[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023773	0.97[EUR][1000 genomes]
rs17446102	0.85[CEU][hapmap];0.94[EUR][1000 genomes]
rs17446515	0.85[CEU][hapmap];0.94[EUR][1000 genomes]
rs17446690	0.85[CEU][hapmap];0.94[EUR][1000 genomes]
rs17505580	0.94[EUR][1000 genomes]
rs17505877	0.94[EUR][1000 genomes]
rs2056653	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056655	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2111383	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2373530	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs2373532	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732052	1.00[EUR][1000 genomes]
rs4670938	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55761128	1.00[EUR][1000 genomes]
rs6544227	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6544229	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6720537	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6720951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6721049	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6721740	0.97[EUR][1000 genomes]
rs6731310	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6758596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73924009	1.00[EUR][1000 genomes]
rs7559436	1.00[EUR][1000 genomes]
rs7577097	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7588265	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs7596222	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs7605939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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	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:111 , 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	chr2:39652000-39662400	Weak transcription	Esophagus	oesophagus
3	chr2:39652000-39662400	Weak transcription	Lung	lung
4	chr2:39652400-39661200	Weak transcription	HUVEC	blood vessel
5	chr2:39652800-39661400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:39652800-39661400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:39652800-39661600	Weak transcription	Fetal Thymus	thymus
8	chr2:39654400-39660400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:39655200-39660400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:39656600-39660600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr2:39656600-39660800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:39656600-39661200	Enhancers	Fetal Heart	heart
13	chr2:39656600-39661800	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr2:39656600-39662200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:39657200-39661200	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr2:39657400-39660800	Weak transcription	NH-A	brain
17	chr2:39657400-39661600	Enhancers	Adipose Nuclei	Adipose
18	chr2:39657600-39660600	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr2:39657600-39661200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:39657800-39660800	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr2:39657800-39661000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr2:39657800-39661600	Enhancers	NHDF-Ad	bronchial
23	chr2:39657800-39661800	Enhancers	Colon Smooth Muscle	Colon
24	chr2:39657800-39662400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr2:39658000-39660400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr2:39658000-39661400	Enhancers	HSMMtube	muscle
27	chr2:39658000-39661600	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr2:39658000-39661600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:39658000-39662400	Enhancers	Liver	Liver
30	chr2:39658200-39660400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:39658200-39661200	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr2:39658200-39661600	Enhancers	Hela-S3	cervix
33	chr2:39658200-39662400	Enhancers	H1 Cell Line	embryonic stem cell
34	chr2:39658400-39661800	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr2:39658400-39662400	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr2:39658600-39660400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr2:39658600-39661000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr2:39658600-39662800	Enhancers	Stomach Mucosa	stomach
39	chr2:39658600-39663000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr2:39658800-39660600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:39658800-39660600	Weak transcription	Fetal Brain Male	brain
42	chr2:39658800-39660800	Weak transcription	Gastric	stomach
43	chr2:39659000-39661600	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr2:39659000-39663000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:39659200-39660800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:39659200-39660800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:39659200-39660800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:39659200-39660800	Weak transcription	Fetal Muscle Leg	muscle
49	chr2:39659200-39660800	Weak transcription	Placenta	Placenta
50	chr2:39659200-39660800	Weak transcription	Stomach Smooth Muscle	stomach

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