Variant report

Variant	rs430431
Chromosome Location	chr4:129195296-129195297
allele	A/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	CTCF	chr4:129195220-129195370	AG09319	gingival:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:129191253..129196346-chr4:129207111..129210585,6	MCF-7	breast:
2	chr4:129147470..129151366-chr4:129195142..129198204,3	MCF-7	breast:

Variant related genes	Relation type
PGRMC2	TF binding region
ENSG00000164040	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11098953	0.87[ASN][1000 genomes]
rs11098954	0.83[CEU][hapmap];0.87[ASN][1000 genomes]
rs11728141	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11733374	0.89[EUR][1000 genomes]
rs12650034	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13103317	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13103695	0.89[EUR][1000 genomes]
rs1391980	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1403125	0.89[EUR][1000 genomes]
rs1522432	0.89[EUR][1000 genomes]
rs1829726	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1851399	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1851400	0.89[EUR][1000 genomes]
rs2036687	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2101808	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2202805	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2391257	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28609279	0.88[ASN][1000 genomes]
rs290004	0.83[ASN][1000 genomes]
rs34174952	0.89[EUR][1000 genomes]
rs34837036	0.85[ASN][1000 genomes]
rs3755896	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4624668	0.89[EUR][1000 genomes]
rs4975180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4975220	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4975299	0.86[ASN][1000 genomes]
rs62318161	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6814132	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6816625	0.88[ASN][1000 genomes]
rs6842987	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6849992	0.88[ASN][1000 genomes]
rs7666566	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7679633	0.89[EUR][1000 genomes]
rs7691103	0.89[EUR][1000 genomes]
rs9790593	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390887	chr4:128932563-129207255	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129173800-129207400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:129184600-129206200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr4:129187800-129206400	Weak transcription	Ovary	ovary
4	chr4:129187800-129206600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:129187800-129207200	Weak transcription	Aorta	Aorta
6	chr4:129188600-129205800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr4:129188800-129203600	Weak transcription	Stomach Mucosa	stomach
8	chr4:129188800-129206200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:129189000-129200800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr4:129189000-129205600	Weak transcription	Fetal Lung	lung
11	chr4:129189400-129198800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:129189400-129206000	Weak transcription	Fetal Stomach	stomach
13	chr4:129189400-129207200	Weak transcription	Thymus	Thymus
14	chr4:129189600-129200800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:129189800-129195400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:129189800-129205400	Weak transcription	Colon Smooth Muscle	Colon
17	chr4:129190000-129195400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:129190000-129197000	Weak transcription	Pancreas	Pancrea
19	chr4:129190000-129206000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr4:129190200-129195400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:129190200-129195600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:129190200-129200400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr4:129190400-129201000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:129190600-129195400	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:129190600-129195400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:129190600-129195400	Strong transcription	HMEC	breast
27	chr4:129190600-129198000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:129190600-129205400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:129190600-129206200	Weak transcription	Psoas Muscle	Psoas
30	chr4:129190600-129206600	Weak transcription	Brain Anterior Caudate	brain
31	chr4:129190800-129195400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:129190800-129195800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:129190800-129195800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:129191000-129195800	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:129191000-129195800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr4:129191000-129206200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:129191200-129195600	Strong transcription	Dnd41	blood
38	chr4:129191200-129197600	Weak transcription	Small Intestine	intestine
39	chr4:129191400-129207800	Weak transcription	Esophagus	oesophagus
40	chr4:129191600-129200600	Weak transcription	Fetal Brain Female	brain
41	chr4:129191600-129206600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr4:129191600-129207400	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:129191800-129205400	Weak transcription	Fetal Brain Male	brain
44	chr4:129192000-129196200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:129192200-129197000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr4:129192400-129200600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr4:129192400-129205800	Weak transcription	Fetal Kidney	kidney
48	chr4:129192400-129206200	Weak transcription	Brain Germinal Matrix	brain
49	chr4:129192600-129207800	Weak transcription	Lung	lung
50	chr4:129192800-129206200	Weak transcription	Primary B cells from cord blood	blood

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