Variant report

Variant	rs10011798
Chromosome Location	chr4:87812564-87812565
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87515391..87517685-chr4:87812251..87815383,4	MCF-7	breast:
2	chr4:87514124..87517809-chr4:87811943..87814768,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109339	Chromatin interaction
ENSG00000163629	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10015121	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10015477	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10015508	0.86[YRI][hapmap]
rs10021020	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10021790	0.85[ASN][1000 genomes]
rs10034336	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1010902	0.97[ASN][1000 genomes]
rs1010903	0.97[ASN][1000 genomes]
rs11097123	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11097125	1.00[EUR][1000 genomes]
rs12503045	1.00[EUR][1000 genomes]
rs12507165	1.00[EUR][1000 genomes]
rs12641570	1.00[EUR][1000 genomes]
rs13115795	0.96[ASN][1000 genomes]
rs13120981	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13137483	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1374935	0.98[EUR][1000 genomes]
rs17012132	0.86[ASN][1000 genomes]
rs17751557	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs1868244	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs1985944	0.97[ASN][1000 genomes]
rs2121871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2594274	0.98[EUR][1000 genomes]
rs2594283	0.94[EUR][1000 genomes]
rs2705629	0.99[EUR][1000 genomes]
rs28446826	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28641910	1.00[ASN][1000 genomes]
rs28650493	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28716151	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2904148	0.94[EUR][1000 genomes]
rs2904150	0.98[EUR][1000 genomes]
rs35428486	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4235082	0.99[EUR][1000 genomes]
rs4693154	0.90[JPT][hapmap]
rs55698195	0.88[ASN][1000 genomes]
rs55889191	0.95[EUR][1000 genomes]
rs56062410	0.91[EUR][1000 genomes]
rs56201068	0.92[ASN][1000 genomes]
rs67758970	1.00[EUR][1000 genomes]
rs6823051	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6843070	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs6846822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72667703	0.97[ASN][1000 genomes]
rs72667705	0.96[ASN][1000 genomes]
rs727143	0.86[YRI][hapmap]

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	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv508297	chr4:87778783-87868508	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87804200-87812600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr4:87806800-87812600	Weak transcription	Adipose Nuclei	Adipose
3	chr4:87806800-87813000	Weak transcription	Left Ventricle	heart
4	chr4:87807200-87812800	Weak transcription	Brain Anterior Caudate	brain
5	chr4:87808200-87812600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:87811800-87812600	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr4:87811800-87812600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr4:87811800-87812600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:87811800-87812600	Enhancers	Duodenum Mucosa	Duodenum
10	chr4:87811800-87812600	Enhancers	Fetal Brain Female	brain
11	chr4:87811800-87812600	Flanking Active TSS	HMEC	breast
12	chr4:87811800-87812800	Flanking Active TSS	Fetal Lung	lung
13	chr4:87811800-87813000	Flanking Active TSS	NHEK	skin
14	chr4:87812000-87812600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:87812000-87812600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:87812000-87812600	Enhancers	Brain Hippocampus Middle	brain
17	chr4:87812000-87812600	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr4:87812000-87812600	Enhancers	Stomach Mucosa	stomach
19	chr4:87812000-87812800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:87812000-87812800	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr4:87812000-87812800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr4:87812000-87812800	Enhancers	Brain Germinal Matrix	brain
23	chr4:87812000-87812800	Enhancers	Brain Substantia Nigra	brain
24	chr4:87812000-87812800	Enhancers	Placenta	Placenta
25	chr4:87812000-87812800	Enhancers	HUVEC	blood vessel
26	chr4:87812000-87813800	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr4:87812000-87814400	Active TSS	Esophagus	oesophagus
28	chr4:87812200-87812600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:87812200-87812600	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr4:87812200-87812600	Enhancers	Fetal Intestine Large	intestine
31	chr4:87812200-87812800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr4:87812200-87812800	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr4:87812200-87813000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:87812200-87813000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:87812200-87814000	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr4:87812400-87812600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr4:87812400-87812600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:87812400-87812600	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr4:87812400-87812600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
40	chr4:87812400-87812600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:87812400-87812600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr4:87812400-87812600	Enhancers	Fetal Kidney	kidney
43	chr4:87812400-87812600	Weak transcription	Pancreas	Pancrea
44	chr4:87812400-87812600	Enhancers	Placenta Amnion	Placenta Amnion
45	chr4:87812400-87812600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr4:87812400-87812600	Enhancers	A549	lung
47	chr4:87812400-87812800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr4:87812400-87812800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
49	chr4:87812400-87812800	Enhancers	NHDF-Ad	bronchial
50	chr4:87812400-87813000	ZNF genes & repeats	Fetal Brain Male	brain

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