Variant report

Variant	rs9848659
Chromosome Location	chr3:93760824-93760825
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	chr3:93759096..93761629-chr3:93781642..93783414,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178700	Chromatin interaction
ENSG00000178694	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs4535269	0.81[EUR][1000 genomes]
rs4857173	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6771653	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6786905	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9821535	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9843295	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869241	chr3:93527675-94504491	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv998173	chr3:93575084-94427403	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv536644	chr3:93575084-94427403	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1008711	chr3:93575284-94427264	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv536646	chr3:93575284-94427264	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv491829	chr3:93575285-94427263	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv1795060	chr3:93602038-93848525	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
8	esv1791740	chr3:93602927-93849247	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
9	esv2755326	chr3:93605126-93882750	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	n/a
10	nsv1013107	chr3:93654100-94102212	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv536648	chr3:93654100-94102212	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1004176	chr3:93654100-94502551	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv590987	chr3:93708820-93779664	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:93699600-93762600	Weak transcription	Pancreas	Pancrea
2	chr3:93708400-93780800	Weak transcription	K562	blood
3	chr3:93708600-93762600	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:93713200-93762200	Weak transcription	HSMM	muscle
5	chr3:93717000-93763000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:93721200-93763200	Weak transcription	Left Ventricle	heart
7	chr3:93721400-93762400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:93723600-93780800	Weak transcription	Fetal Lung	lung
9	chr3:93723600-93780800	Weak transcription	HSMMtube	muscle
10	chr3:93726200-93780800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:93738800-93762600	Weak transcription	Esophagus	oesophagus
12	chr3:93740600-93780800	Weak transcription	NHDF-Ad	bronchial
13	chr3:93743600-93769000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:93743600-93780800	Weak transcription	Aorta	Aorta
15	chr3:93743800-93769600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:93744000-93763000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:93747600-93762600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:93747600-93762800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:93747800-93762800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:93748800-93777600	Weak transcription	A549	lung
21	chr3:93751000-93780600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:93751400-93763200	Weak transcription	Gastric	stomach
23	chr3:93751600-93762600	Weak transcription	Fetal Stomach	stomach
24	chr3:93753000-93762600	Weak transcription	Brain Germinal Matrix	brain
25	chr3:93753200-93778000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:93753800-93762600	Weak transcription	Adipose Nuclei	Adipose
27	chr3:93753800-93780800	Weak transcription	HUVEC	blood vessel
28	chr3:93754200-93763200	Weak transcription	Ovary	ovary
29	chr3:93754200-93763400	Weak transcription	Brain Hippocampus Middle	brain
30	chr3:93754200-93781000	Weak transcription	Small Intestine	intestine
31	chr3:93754400-93780800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:93754800-93763000	Weak transcription	Right Ventricle	heart
33	chr3:93754800-93763200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr3:93755000-93761800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:93755000-93763000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:93755400-93761000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:93755600-93762600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:93755800-93780800	Weak transcription	Primary B cells from cord blood	blood
39	chr3:93756000-93762600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:93756200-93761600	Weak transcription	Dnd41	blood
41	chr3:93756200-93763000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:93756200-93778800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:93756200-93780600	Weak transcription	GM12878-XiMat	blood
44	chr3:93756200-93780800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr3:93756200-93780800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr3:93756200-93780800	Weak transcription	NHEK	skin
47	chr3:93756200-93780800	Weak transcription	Osteobl	bone
48	chr3:93756600-93762600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:93756600-93762600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:93756600-93778600	Weak transcription	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links