Variant report

Variant	rs62410604
Chromosome Location	chr3:196305618-196305619
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196302803..196305779-chr3:196318881..196320919,2	K562	blood:
2	chr3:196304153..196307094-chr3:196308017..196309904,2	MCF-7	breast:
3	chr3:196294278..196297530-chr3:196305602..196308236,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185798	Chromatin interaction
ENSG00000174013	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs55935991	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57065452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58145658	1.00[AFR][1000 genomes]
rs61138270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62410571	1.00[EUR][1000 genomes]
rs62410605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62410606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62410621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62410622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62410623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6583321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6763065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6781434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6791388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6794350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6799134	1.00[EUR][1000 genomes]
rs6804773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7611228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7639349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7653049	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv1010483	chr3:196210054-196319543	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv536896	chr3:196210054-196319543	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv491864	chr3:196263064-196468533	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats 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	43 gene(s)	inside rSNPs	diseases
10	nsv829828	chr3:196268121-196463641	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
11	nsv1010643	chr3:196288064-196788645	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 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	chr3:196296400-196311000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:196296600-196320200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:196296800-196305800	Weak transcription	HSMM	muscle
4	chr3:196296800-196311000	Weak transcription	Placenta	Placenta
5	chr3:196296800-196316800	Weak transcription	Right Ventricle	heart
6	chr3:196297000-196307200	Weak transcription	Esophagus	oesophagus
7	chr3:196297000-196307200	Weak transcription	Spleen	Spleen
8	chr3:196297000-196307400	Weak transcription	Aorta	Aorta
9	chr3:196297000-196310000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:196297000-196310800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:196297000-196311000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:196297000-196311000	Weak transcription	NH-A	brain
13	chr3:196297000-196314400	Weak transcription	Brain Anterior Caudate	brain
14	chr3:196297000-196316000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:196297000-196316200	Weak transcription	Right Atrium	heart
16	chr3:196297000-196317000	Weak transcription	NHLF	lung
17	chr3:196297000-196317800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:196297000-196318000	Weak transcription	Colonic Mucosa	Colon
19	chr3:196297000-196320400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:196297200-196308800	Weak transcription	Brain Substantia Nigra	brain
21	chr3:196297200-196311000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:196297200-196311000	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:196297200-196311000	Weak transcription	Stomach Mucosa	stomach
24	chr3:196297200-196311800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:196297200-196312400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:196297200-196313200	Weak transcription	Fetal Kidney	kidney
27	chr3:196297200-196315600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:196297200-196316800	Weak transcription	Brain Angular Gyrus	brain
29	chr3:196297200-196323000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:196297400-196305800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr3:196297400-196311000	Weak transcription	Primary B cells from cord blood	blood
32	chr3:196297400-196311000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:196297400-196311000	Weak transcription	Fetal Heart	heart
34	chr3:196297400-196311000	Weak transcription	Gastric	stomach
35	chr3:196297400-196311000	Weak transcription	Psoas Muscle	Psoas
36	chr3:196297400-196313800	Weak transcription	Small Intestine	intestine
37	chr3:196297400-196318800	Weak transcription	Pancreas	Pancrea
38	chr3:196297600-196307400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:196298000-196307600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:196298000-196319400	Weak transcription	Fetal Brain Male	brain
41	chr3:196298400-196307000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:196298600-196307600	Weak transcription	Brain Germinal Matrix	brain
43	chr3:196298600-196313000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:196298800-196308200	Weak transcription	HUVEC	blood vessel
45	chr3:196299600-196311200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:196300400-196307400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr3:196302400-196308200	Weak transcription	A549	lung
48	chr3:196302800-196306800	Strong transcription	K562	blood
49	chr3:196303000-196311600	Strong transcription	Primary T cells from cord blood	blood
50	chr3:196303400-196316400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links