Variant report

Variant	rs35512962
Chromosome Location	chr3:46964735-46964736
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46951194..46952854-chr3:46962905..46965136,2	MCF-7	breast:
2	chr3:46963604..46965379-chr3:47041668..47043184,2	K562	blood:
3	chr3:46959572..46964744-chr3:47019685..47022542,4	K562	blood:
4	chr3:46962117..46964738-chr3:47204547..47206100,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MYL3-1	chr3:46963238-46965649	NONHSAT089464

Variant related genes	Relation type
ENSG00000181555	Chromatin interaction
ENSG00000160799	Chromatin interaction
ENSG00000160796	Chromatin interaction
ENSG00000227398	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12715420	1.00[EUR][1000 genomes]
rs13060505	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs33983156	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34207078	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35194354	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35418672	0.83[EUR][1000 genomes]
rs71327102	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71328903	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7624740	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936183	0.84[AMR][1000 genomes]
rs9841902	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv876752	chr3:46879831-46967040	Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv876754	chr3:46884552-46967040	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv460526	chr3:46935527-47001350	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv3800	chr3:46961648-47007241	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46955800-46964800	Weak transcription	Right Atrium	heart
2	chr3:46956400-46965200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr3:46956600-46967200	Strong transcription	Thymus	Thymus
4	chr3:46956800-46966600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr3:46957000-46965400	Strong transcription	Fetal Muscle Trunk	muscle
6	chr3:46957200-46964800	Weak transcription	Fetal Heart	heart
7	chr3:46957800-46966600	Strong transcription	Fetal Thymus	thymus
8	chr3:46957800-46967200	Strong transcription	HSMM	muscle
9	chr3:46958200-46964800	Strong transcription	Placenta Amnion	Placenta Amnion
10	chr3:46958200-46966800	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr3:46958200-46967200	Strong transcription	Muscle Satellite Cultured Cells	--
12	chr3:46958200-46967600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr3:46958200-46968200	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr3:46958200-46968800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:46958400-46965200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:46958400-46965200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:46958400-46966800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:46958400-46967200	Strong transcription	HMEC	breast
19	chr3:46958400-46967600	Strong transcription	Primary T cells from cord blood	blood
20	chr3:46958400-46967800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:46958400-46968200	Strong transcription	Dnd41	blood
22	chr3:46958600-46964800	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr3:46958600-46965000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:46958600-46965200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:46958600-46965200	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:46958600-46965200	Strong transcription	Fetal Intestine Large	intestine
27	chr3:46958600-46965600	Strong transcription	Duodenum Mucosa	Duodenum
28	chr3:46958600-46966400	Strong transcription	Placenta	Placenta
29	chr3:46958600-46966600	Strong transcription	Adipose Nuclei	Adipose
30	chr3:46958600-46966800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:46958600-46966800	Strong transcription	HSMMtube	muscle
32	chr3:46958600-46967000	Strong transcription	Brain Anterior Caudate	brain
33	chr3:46958600-46967200	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:46958600-46967400	Strong transcription	Liver	Liver
35	chr3:46958600-46967800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:46958600-46968000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:46958600-46970200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:46958800-46965000	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:46958800-46965000	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr3:46958800-46965400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:46958800-46967200	Strong transcription	NH-A	brain
42	chr3:46958800-46967600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:46958800-46967600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:46958800-46967800	Strong transcription	Osteobl	bone
45	chr3:46959000-46965200	Strong transcription	Primary hematopoietic stem cells	blood
46	chr3:46959000-46971400	Strong transcription	K562	blood
47	chr3:46959400-46966600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:46959400-46967200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr3:46959400-46967200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:46959400-46967200	Strong transcription	Brain Angular Gyrus	brain

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