Variant report

Variant	rs13129077
Chromosome Location	chr4:8458394-8458395
allele	A/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	POLR2A	chr4:8457877-8458512	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:8457452..8459896-chr4:8461830..8464579,3	K562	blood:
2	chr4:8442603..8444779-chr4:8457988..8460939,2	MCF-7	breast:
3	chr4:8458147..8460116-chr4:8460485..8462982,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251186	TF binding region
ENSG00000155275	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10938716	0.88[ASN][1000 genomes]
rs10938717	0.88[ASN][1000 genomes]
rs13105415	0.88[ASN][1000 genomes]
rs13105907	0.92[ASN][1000 genomes]
rs13106582	0.86[ASN][1000 genomes]
rs13111630	0.88[ASN][1000 genomes]
rs13120514	0.88[ASN][1000 genomes]
rs13120605	0.92[ASN][1000 genomes]
rs13121817	0.92[ASN][1000 genomes]
rs13122276	0.92[ASN][1000 genomes]
rs13132875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13141535	0.92[ASN][1000 genomes]
rs13147943	0.89[ASN][1000 genomes]
rs16842355	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2293230	0.86[JPT][hapmap]
rs34053441	0.81[ASN][1000 genomes]
rs34465110	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs34681013	0.93[AFR][1000 genomes]
rs34935132	0.94[ASN][1000 genomes]
rs35769879	0.93[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs36122693	0.88[ASN][1000 genomes]
rs3775895	0.90[ASN][1000 genomes]
rs3796744	0.86[JPT][hapmap]
rs3796747	0.86[JPT][hapmap]
rs3796763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3806811	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822207	0.86[JPT][hapmap]
rs4481223	0.86[JPT][hapmap]
rs56786736	0.92[ASN][1000 genomes]
rs60080531	0.92[ASN][1000 genomes]
rs6811968	0.90[ASN][1000 genomes]
rs6813502	0.90[ASN][1000 genomes]
rs6816430	0.90[ASN][1000 genomes]
rs6832505	0.93[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6832668	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs73089514	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670021	0.88[ASN][1000 genomes]
rs7697154	0.88[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs940135	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv461220	chr4:8372944-8458394	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv593638	chr4:8372944-8458394	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8444800-8458400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:8445000-8460800	Weak transcription	Psoas Muscle	Psoas
3	chr4:8445200-8461400	Weak transcription	Hela-S3	cervix
4	chr4:8446400-8463200	Strong transcription	Stomach Smooth Muscle	stomach
5	chr4:8446400-8473800	Strong transcription	Fetal Stomach	stomach
6	chr4:8446600-8463600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr4:8446600-8463600	Strong transcription	Thymus	Thymus
8	chr4:8446600-8464600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:8446600-8473400	Strong transcription	Dnd41	blood
10	chr4:8446600-8474000	Strong transcription	Fetal Muscle Leg	muscle
11	chr4:8446800-8463800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:8447000-8461800	Strong transcription	Fetal Intestine Large	intestine
13	chr4:8447000-8464000	Strong transcription	Primary B cells from cord blood	blood
14	chr4:8447000-8474400	Strong transcription	Fetal Brain Female	brain
15	chr4:8447000-8475200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:8447000-8480200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:8447200-8464200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr4:8447200-8473000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr4:8447200-8480200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr4:8447400-8463600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:8447400-8474000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:8447400-8482200	Strong transcription	Primary T cells from cord blood	blood
23	chr4:8447600-8464000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr4:8447600-8472200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr4:8447600-8473400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr4:8447800-8458400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:8447800-8459800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr4:8447800-8461200	Strong transcription	Liver	Liver
29	chr4:8447800-8461800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:8447800-8463400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr4:8447800-8463400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:8447800-8463600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr4:8447800-8463800	Strong transcription	Brain Cingulate Gyrus	brain
34	chr4:8447800-8472800	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr4:8448000-8461400	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr4:8448000-8461600	Strong transcription	Duodenum Mucosa	Duodenum
37	chr4:8448000-8461800	Strong transcription	Primary B cells from peripheral blood	blood
38	chr4:8448000-8462000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:8448000-8463200	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr4:8448000-8463600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr4:8448200-8463800	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr4:8448200-8467400	Strong transcription	Adipose Nuclei	Adipose
43	chr4:8449000-8461600	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr4:8449400-8460000	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr4:8449400-8460200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:8449600-8461400	Strong transcription	Fetal Thymus	thymus
47	chr4:8449600-8463600	Strong transcription	Spleen	Spleen
48	chr4:8449800-8461000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr4:8450000-8458600	Strong transcription	GM12878-XiMat	blood
50	chr4:8450200-8460800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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