Variant report

Variant	rs7624777
Chromosome Location	chr3:105234139-105234140
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	chr3:105085752..105088107-chr3:105232298..105234295,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170017	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10511244	0.82[MKK][hapmap]
rs12632847	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16851188	0.82[MKK][hapmap]
rs16851303	0.82[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap]
rs56180821	0.84[ASN][1000 genomes]
rs58582466	0.85[ASN][1000 genomes]
rs73006164	0.81[AFR][1000 genomes]
rs9637375	0.82[MKK][hapmap]
rs9842815	0.81[AFR][1000 genomes]
rs9843750	1.00[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][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	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv829651	chr3:105203424-105402136	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv460811	chr3:105212993-105316769	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv591240	chr3:105212993-105316769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105210200-105243200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:105221400-105300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:105222200-105260600	Weak transcription	Fetal Kidney	kidney
4	chr3:105222800-105246000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:105223800-105274800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:105224400-105239600	Weak transcription	GM12878-XiMat	blood
7	chr3:105225800-105236000	Weak transcription	Liver	Liver
8	chr3:105229600-105244600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:105229600-105260400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:105229800-105235000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:105230000-105234200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:105230200-105262600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:105230400-105234200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:105230800-105234200	Weak transcription	Brain Angular Gyrus	brain
15	chr3:105231000-105237400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:105231400-105234200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:105231800-105234600	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr3:105232000-105234600	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr3:105232200-105245400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:105232200-105245400	Weak transcription	NHEK	skin
21	chr3:105232200-105245600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:105232200-105274000	Weak transcription	HSMMtube	muscle
23	chr3:105232400-105237600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:105232400-105237600	Weak transcription	Fetal Heart	heart
25	chr3:105232600-105234200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:105232600-105242400	Weak transcription	NHLF	lung
27	chr3:105232800-105236000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:105232800-105243200	Weak transcription	NH-A	brain
29	chr3:105233000-105234200	Weak transcription	Brain Anterior Caudate	brain
30	chr3:105233000-105235800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:105233000-105237800	Enhancers	A549	lung
32	chr3:105233200-105234200	Weak transcription	Osteobl	bone
33	chr3:105233200-105236000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr3:105233200-105237600	Weak transcription	NHDF-Ad	bronchial
35	chr3:105233200-105243200	Weak transcription	HMEC	breast
36	chr3:105233400-105234600	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr3:105233400-105237600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:105233400-105250600	Weak transcription	HSMM	muscle
39	chr3:105233600-105234400	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr3:105233600-105234800	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr3:105233600-105237400	Enhancers	Brain Hippocampus Middle	brain
42	chr3:105233800-105234600	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr3:105233800-105237800	Enhancers	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links