Variant report

Variant	rs1078646
Chromosome Location	chr5:179778098-179778099
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179775628..179778352-chr5:179778745..179780762,2	MCF-7	breast:
2	chr5:179776807..179778775-chr5:179896611..179898165,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131459	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1559114	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17080196	0.87[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs17080199	0.87[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs2303012	0.87[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs4235511	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4566752	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4700736	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4700943	0.89[ASN][1000 genomes]
rs62404950	0.89[ASN][1000 genomes]
rs62404953	0.98[ASN][1000 genomes]
rs62404956	0.98[ASN][1000 genomes]
rs62404958	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62404959	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406364	0.94[ASN][1000 genomes]
rs6601110	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6859159	0.87[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs6864729	0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs6870028	0.89[ASN][1000 genomes]
rs6871454	0.88[ASN][1000 genomes]
rs6874176	0.89[ASN][1000 genomes]
rs6884276	0.94[ASN][1000 genomes]
rs6899097	0.96[ASN][1000 genomes]
rs72811045	0.89[ASN][1000 genomes]
rs72811049	0.89[ASN][1000 genomes]
rs9686940	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
5	nsv883290	chr5:179712060-179818868	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv830563	chr5:179717693-179898609	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv1031836	chr5:179742033-180676122	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
9	nsv537984	chr5:179742033-180676122	Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
10	nsv949199	chr5:179743553-180696889	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
11	nsv883291	chr5:179755559-179818868	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv984575	chr5:179759624-179791220	Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179757000-179779000	Weak transcription	Esophagus	oesophagus
2	chr5:179764000-179778800	Weak transcription	Pancreas	Pancrea
3	chr5:179770400-179779000	Weak transcription	Gastric	stomach
4	chr5:179770600-179778600	Weak transcription	Right Atrium	heart
5	chr5:179771200-179778600	Weak transcription	Lung	lung
6	chr5:179771600-179778400	Weak transcription	HSMM	muscle
7	chr5:179771600-179778600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:179771600-179778600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:179771800-179778400	Weak transcription	Hela-S3	cervix
10	chr5:179771800-179778600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:179772600-179779200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr5:179773600-179778400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:179775000-179778200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:179775400-179778600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr5:179775400-179778600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:179776600-179778600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr5:179776600-179778600	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr5:179776800-179778800	Enhancers	Brain Angular Gyrus	brain
19	chr5:179777000-179778600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr5:179777000-179778800	Enhancers	Brain Hippocampus Middle	brain
21	chr5:179777000-179778800	Bivalent Enhancer	Fetal Muscle Leg	muscle
22	chr5:179777000-179779000	Enhancers	Brain Substantia Nigra	brain
23	chr5:179777000-179779200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
24	chr5:179777000-179779200	Bivalent Enhancer	Placenta	Placenta
25	chr5:179777200-179778600	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr5:179777200-179778600	Weak transcription	Ovary	ovary
27	chr5:179777200-179778800	Weak transcription	Left Ventricle	heart
28	chr5:179777400-179778200	Enhancers	H9 Cell Line	embryonic stem cell
29	chr5:179777400-179778200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:179777400-179778600	Enhancers	Brain Anterior Caudate	brain
31	chr5:179777400-179778600	Enhancers	Brain Cingulate Gyrus	brain
32	chr5:179777400-179778600	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr5:179777400-179778800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr5:179777400-179778800	Bivalent Enhancer	Fetal Stomach	stomach
35	chr5:179777400-179778800	Enhancers	HSMMtube	muscle
36	chr5:179777600-179778200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:179777600-179778200	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
38	chr5:179777600-179778200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr5:179777600-179778400	Enhancers	Muscle Satellite Cultured Cells	--
40	chr5:179777600-179778400	Enhancers	Osteobl	bone
41	chr5:179777600-179778600	Enhancers	A549	lung
42	chr5:179777600-179779000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr5:179777600-179779000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr5:179777600-179779600	Active TSS	Right Ventricle	heart
45	chr5:179777800-179778200	Enhancers	H1 Cell Line	embryonic stem cell
46	chr5:179777800-179778200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr5:179777800-179778200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:179777800-179778600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr5:179777800-179778600	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr5:179777800-179778600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links