Variant report

Variant	rs56004331
Chromosome Location	chr3:105578969-105578970
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105578910..105582345-chr3:105586229..105588462,4	MCF-7	breast:
2	chr3:105577086..105579511-chr3:105584750..105588658,3	K562	blood:

Variant related genes	Relation type
ENSG00000114423	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs55857799	1.00[AMR][1000 genomes]
rs55949717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56072602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56122972	1.00[AMR][1000 genomes]
rs56249671	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56256418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56696279	1.00[AMR][1000 genomes]
rs57184464	1.00[AMR][1000 genomes]
rs58846261	1.00[AMR][1000 genomes]
rs58991769	1.00[AMR][1000 genomes]
rs59294274	1.00[AMR][1000 genomes]
rs59347770	1.00[AMR][1000 genomes]
rs59577696	1.00[AMR][1000 genomes]
rs59924993	1.00[AMR][1000 genomes]
rs61115724	1.00[AMR][1000 genomes]
rs61230240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61452551	1.00[AMR][1000 genomes]
rs73854349	1.00[AMR][1000 genomes]
rs73854350	1.00[AMR][1000 genomes]
rs73854352	1.00[AMR][1000 genomes]
rs73854353	1.00[AMR][1000 genomes]
rs73854354	1.00[AMR][1000 genomes]
rs73854355	1.00[AMR][1000 genomes]
rs73854356	1.00[AMR][1000 genomes]
rs73854359	1.00[AMR][1000 genomes]
rs73854361	1.00[AMR][1000 genomes]
rs73854378	1.00[AMR][1000 genomes]
rs73854385	1.00[AMR][1000 genomes]
rs73854389	1.00[AMR][1000 genomes]
rs73854390	1.00[AMR][1000 genomes]
rs73854392	1.00[AMR][1000 genomes]
rs73854393	1.00[AMR][1000 genomes]
rs73854395	1.00[AMR][1000 genomes]
rs73854396	1.00[AMR][1000 genomes]
rs73854397	1.00[AMR][1000 genomes]
rs73854402	1.00[AMR][1000 genomes]
rs73854884	1.00[AMR][1000 genomes]
rs73854886	1.00[AMR][1000 genomes]
rs73854889	1.00[AMR][1000 genomes]
rs73854892	1.00[AMR][1000 genomes]
rs73855350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73855352	1.00[AMR][1000 genomes]
rs73855362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73855363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73855365	1.00[AMR][1000 genomes]
rs73855366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73857223	1.00[AMR][1000 genomes]
rs73857224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1008564	chr3:105554580-105643435	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1008876	chr3:105554580-105645373	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv877312	chr3:105560638-105916506	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105543400-105581200	Weak transcription	Gastric	stomach
2	chr3:105544200-105584600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:105546600-105586200	Weak transcription	Esophagus	oesophagus
4	chr3:105556200-105579000	Weak transcription	Stomach Mucosa	stomach
5	chr3:105557800-105579200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:105557800-105586200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:105558600-105586600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:105561600-105586200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:105562000-105586000	Weak transcription	K562	blood
10	chr3:105563000-105584600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:105563000-105586800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:105563400-105583000	Weak transcription	Spleen	Spleen
13	chr3:105563800-105584400	Weak transcription	Brain Angular Gyrus	brain
14	chr3:105564800-105585000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:105565600-105584800	Weak transcription	NHEK	skin
16	chr3:105566200-105584800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:105566200-105585000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:105566600-105581200	Weak transcription	Aorta	Aorta
19	chr3:105566600-105584600	Weak transcription	Fetal Stomach	stomach
20	chr3:105567000-105583000	Weak transcription	Brain Substantia Nigra	brain
21	chr3:105567000-105584200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:105567200-105583200	Weak transcription	Brain Hippocampus Middle	brain
23	chr3:105567200-105584000	Weak transcription	Brain Anterior Caudate	brain
24	chr3:105567200-105584600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:105568000-105586200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr3:105568000-105586200	Weak transcription	Pancreas	Pancrea
27	chr3:105568600-105579600	Strong transcription	Osteobl	bone
28	chr3:105568800-105579200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:105568800-105586200	Weak transcription	Colonic Mucosa	Colon
30	chr3:105569400-105584000	Weak transcription	A549	lung
31	chr3:105569600-105579600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:105569800-105586200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:105570200-105584200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:105570600-105584200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:105571000-105582200	Weak transcription	Brain Germinal Matrix	brain
36	chr3:105571200-105584600	Weak transcription	NHLF	lung
37	chr3:105572000-105586200	Weak transcription	Lung	lung
38	chr3:105572200-105579000	Weak transcription	Colon Smooth Muscle	Colon
39	chr3:105572200-105581200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr3:105572200-105584200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:105572200-105584600	Weak transcription	HSMMtube	muscle
42	chr3:105572200-105585000	Weak transcription	Thymus	Thymus
43	chr3:105572200-105585400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:105572400-105582800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr3:105572400-105583000	Weak transcription	HMEC	breast
46	chr3:105572600-105580400	Weak transcription	Fetal Heart	heart
47	chr3:105572600-105582800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr3:105572600-105582800	Weak transcription	Dnd41	blood
49	chr3:105572600-105585200	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr3:105572600-105585800	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links