Variant report

Variant	rs4631734
Chromosome Location	chr1:171220236-171220237
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171219827..171222241-chr1:171222983..171225833,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206692	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10912616	0.96[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12065544	0.95[ASN][1000 genomes]
rs12402732	0.96[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12403890	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12720462	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16864174	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16864177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16864194	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16864216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1987921	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1987944	0.97[ASN][1000 genomes]
rs2020863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2049920	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2064077	0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2072755	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2075988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2179106	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28369891	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28369914	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3861947	0.95[ASN][1000 genomes]
rs4073692	0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4073693	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4622096	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56370691	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs57305992	0.96[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61815363	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61815421	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61815423	0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61815424	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61815425	0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61815427	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72714167	0.96[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7533889	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs7535210	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7551934	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription 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 miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171200800-171220400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:171217200-171220400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:171217200-171220400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:171217600-171221000	Active TSS	Fetal Intestine Small	intestine
5	chr1:171217600-171221200	Active TSS	Fetal Intestine Large	intestine
6	chr1:171219000-171220400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:171219600-171221200	Active TSS	Fetal Lung	lung
8	chr1:171219800-171220600	Bivalent/Poised TSS	Fetal Kidney	kidney
9	chr1:171220000-171220400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr1:171220000-171220400	Bivalent Enhancer	HepG2	liver
11	chr1:171220000-171220800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr1:171220000-171221200	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr1:171220200-171220400	Active TSS	H1 Cell Line	embryonic stem cell
14	chr1:171220200-171220400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr1:171220200-171220400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
16	chr1:171220200-171220400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
17	chr1:171220200-171220400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr1:171220200-171220400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:171220200-171220400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
20	chr1:171220200-171220400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
21	chr1:171220200-171220400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:171220200-171220400	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:171220200-171220400	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:171220200-171220400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:171220200-171220400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:171220200-171220400	Active TSS	Brain Anterior Caudate	brain
27	chr1:171220200-171220400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:171220200-171220400	Enhancers	Colonic Mucosa	Colon
29	chr1:171220200-171220400	Active TSS	Duodenum Mucosa	Duodenum
30	chr1:171220200-171220400	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr1:171220200-171220400	Active TSS	Fetal Muscle Trunk	muscle
32	chr1:171220200-171220400	Bivalent/Poised TSS	Fetal Stomach	stomach
33	chr1:171220200-171220400	Enhancers	Lung	lung
34	chr1:171220200-171220400	Active TSS	Pancreas	Pancrea
35	chr1:171220200-171220400	Enhancers	Placenta Amnion	Placenta Amnion
36	chr1:171220200-171220400	Enhancers	Stomach Mucosa	stomach
37	chr1:171220200-171220400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
38	chr1:171220200-171220400	Active TSS	GM12878-XiMat	blood
39	chr1:171220200-171220400	Enhancers	HMEC	breast
40	chr1:171220200-171220600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:171220200-171220600	Flanking Active TSS	Primary B cells from peripheral blood	blood
42	chr1:171220200-171220600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
43	chr1:171220200-171220600	Flanking Active TSS	Liver	Liver
44	chr1:171220200-171220600	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr1:171220200-171220600	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr1:171220200-171220800	Active TSS	H9 Cell Line	embryonic stem cell
47	chr1:171220200-171220800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:171220200-171220800	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
49	chr1:171220200-171220800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:171220200-171220800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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