Variant report

Variant	rs6765869
Chromosome Location	chr3:49704729-49704730
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49588369..49592998-chr3:49704328..49708705,5	K562	blood:
2	chr3:49704547..49706836-chr3:49714459..49716398,2	MCF-7	breast:
3	chr3:49704645..49708091-chr3:49709856..49713074,5	MCF-7	breast:
4	chr3:49572703..49574370-chr3:49703529..49706014,2	K562	blood:

Variant related genes	Relation type
ENSG00000164061	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000226913	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1060962	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130212	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11130213	0.85[ASN][1000 genomes]
rs11709525	0.81[ASN][1000 genomes]
rs11710037	0.81[ASN][1000 genomes]
rs11718165	0.91[ASN][1000 genomes]
rs11919311	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12490267	0.86[EUR][1000 genomes]
rs12497288	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13316695	0.81[ASN][1000 genomes]
rs1352890	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1873626	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2005557	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131104	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131109	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2172252	0.81[ASN][1000 genomes]
rs2329020	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2960548	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34762726	0.81[ASN][1000 genomes]
rs35007338	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35404120	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4283605	0.81[ASN][1000 genomes]
rs4855835	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4855847	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4855852	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4855881	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4855883	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4855884	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767878	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6770670	0.81[ASN][1000 genomes]
rs9812791	0.81[ASN][1000 genomes]
rs9823546	0.91[ASN][1000 genomes]
rs9824092	0.81[ASN][1000 genomes]
rs9836291	0.91[ASN][1000 genomes]
rs9858542	0.91[ASN][1000 genomes]
rs9862080	0.81[ASN][1000 genomes]
rs9882740	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1011428	chr3:49649989-49706068	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49685200-49708200	Strong transcription	Brain Germinal Matrix	brain
2	chr3:49685400-49708400	Strong transcription	Fetal Brain Female	brain
3	chr3:49686600-49710600	Weak transcription	Right Atrium	heart
4	chr3:49687600-49705800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:49690400-49710600	Weak transcription	Brain Substantia Nigra	brain
6	chr3:49692200-49710400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:49695200-49710600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:49700000-49710600	Weak transcription	Fetal Brain Male	brain
9	chr3:49701400-49704800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:49701800-49707000	Enhancers	Fetal Muscle Leg	muscle
11	chr3:49702000-49707400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr3:49702400-49705600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:49702400-49710600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:49702800-49707400	Enhancers	Pancreas	Pancrea
15	chr3:49703400-49705200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:49703400-49709400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:49703600-49704800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr3:49703600-49705200	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr3:49703600-49705200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:49703600-49705800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:49703600-49706200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:49703600-49709000	Weak transcription	Placenta	Placenta
23	chr3:49703600-49710600	Weak transcription	Left Ventricle	heart
24	chr3:49703600-49710600	Weak transcription	Right Ventricle	heart
25	chr3:49703600-49710600	Weak transcription	Spleen	Spleen
26	chr3:49703800-49705400	Weak transcription	HMEC	breast
27	chr3:49703800-49705600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:49703800-49706000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:49703800-49710600	Enhancers	Liver	Liver
30	chr3:49703800-49710600	Weak transcription	Brain Hippocampus Middle	brain
31	chr3:49704000-49704800	Enhancers	Fetal Intestine Small	intestine
32	chr3:49704000-49705200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:49704000-49706800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:49704000-49707000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:49704200-49704800	Enhancers	Fetal Intestine Large	intestine
36	chr3:49704200-49710600	Weak transcription	Gastric	stomach
37	chr3:49704400-49704800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:49704400-49705000	Enhancers	H1 Cell Line	embryonic stem cell
39	chr3:49704400-49705000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:49704400-49705000	Genic enhancers	Brain Anterior Caudate	brain
41	chr3:49704400-49705400	Genic enhancers	Brain Inferior Temporal Lobe	brain
42	chr3:49704400-49706000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:49704400-49706200	Enhancers	HSMMtube	muscle
44	chr3:49704400-49710600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:49704600-49705000	Enhancers	HepG2	liver
46	chr3:49704600-49705600	Weak transcription	HSMM	muscle
47	chr3:49704600-49705600	Weak transcription	NH-A	brain
48	chr3:49704600-49706200	Enhancers	Brain Angular Gyrus	brain
49	chr3:49704600-49709000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr3:49704600-49709400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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