Variant report

Variant	rs62419373
Chromosome Location	chr6:88191885-88191886
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	chr6:88117340..88119372-chr6:88190299..88193119,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272514	Chromatin interaction
ENSG00000213204	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10080513	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11962998	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13193193	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13200106	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs13205357	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13206485	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13208550	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs13211720	0.89[AMR][1000 genomes]
rs13213812	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13215013	0.90[AMR][1000 genomes]
rs13216482	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13216724	0.82[AMR][1000 genomes]
rs13216727	0.90[AMR][1000 genomes]
rs16879475	0.82[AMR][1000 genomes]
rs16879490	0.82[AMR][1000 genomes]
rs171399	0.84[AMR][1000 genomes]
rs17504209	0.82[AMR][1000 genomes]
rs17504517	0.90[AMR][1000 genomes]
rs2273130	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34006571	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs34007246	0.90[AMR][1000 genomes]
rs34054042	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34369446	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35056836	0.90[AMR][1000 genomes]
rs35116392	0.90[AMR][1000 genomes]
rs35234062	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35237504	0.82[AMR][1000 genomes]
rs35303040	0.85[AMR][1000 genomes]
rs35593940	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs35679038	0.82[AMR][1000 genomes]
rs35866706	0.90[AMR][1000 genomes]
rs3734908	0.82[AMR][1000 genomes]
rs3757369	0.85[AMR][1000 genomes]
rs3800551	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3823469	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4409162	0.90[AMR][1000 genomes]
rs55766457	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55960393	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59361639	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62417674	0.90[AMR][1000 genomes]
rs62417675	0.90[AMR][1000 genomes]
rs62417676	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs62417692	0.90[AMR][1000 genomes]
rs62417693	0.90[AMR][1000 genomes]
rs62419372	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62419377	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62419378	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7757446	0.82[AMR][1000 genomes]
rs7760840	0.94[EUR][1000 genomes]
rs7770458	0.82[AMR][1000 genomes]
rs9444507	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9450703	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9450714	0.82[AMR][1000 genomes];0.93[EUR][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	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv830722	chr6:88054186-88223625	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers 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	23 gene(s)	inside rSNPs	diseases
5	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88183600-88193000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr6:88183600-88193200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:88183600-88193200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:88183600-88193200	Weak transcription	Lung	lung
5	chr6:88183600-88193400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:88183600-88193600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:88183600-88212800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:88183600-88226000	Weak transcription	Gastric	stomach
9	chr6:88183800-88193000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:88183800-88193000	Weak transcription	Esophagus	oesophagus
11	chr6:88183800-88193000	Weak transcription	Fetal Intestine Small	intestine
12	chr6:88183800-88193200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:88183800-88193200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr6:88183800-88193200	Weak transcription	Placenta	Placenta
15	chr6:88183800-88193600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:88183800-88193800	Weak transcription	Colonic Mucosa	Colon
17	chr6:88183800-88197000	Weak transcription	NH-A	brain
18	chr6:88183800-88204200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr6:88183800-88210800	Weak transcription	Adipose Nuclei	Adipose
20	chr6:88183800-88211000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr6:88183800-88211000	Weak transcription	Brain Anterior Caudate	brain
22	chr6:88183800-88211000	Weak transcription	Thymus	Thymus
23	chr6:88183800-88211800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr6:88183800-88212000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:88183800-88212600	Weak transcription	Psoas Muscle	Psoas
26	chr6:88183800-88216400	Weak transcription	K562	blood
27	chr6:88183800-88219800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr6:88183800-88221000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr6:88183800-88221000	Weak transcription	Fetal Kidney	kidney
30	chr6:88183800-88225400	Weak transcription	Aorta	Aorta
31	chr6:88183800-88227400	Weak transcription	Right Ventricle	heart
32	chr6:88184000-88193400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:88184000-88193400	Weak transcription	Brain Hippocampus Middle	brain
34	chr6:88184000-88200800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:88184000-88202400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:88184000-88210800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr6:88184000-88211000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr6:88184000-88211000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr6:88184000-88218600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:88184000-88218600	Weak transcription	Brain Angular Gyrus	brain
41	chr6:88184000-88218800	Weak transcription	Brain Germinal Matrix	brain
42	chr6:88184000-88219800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr6:88184000-88221000	Weak transcription	Colon Smooth Muscle	Colon
44	chr6:88184000-88224200	Weak transcription	Hela-S3	cervix
45	chr6:88184200-88193400	Weak transcription	HSMM	muscle
46	chr6:88184200-88211000	Weak transcription	NHDF-Ad	bronchial
47	chr6:88184200-88214800	Weak transcription	Fetal Brain Male	brain
48	chr6:88184400-88193000	Weak transcription	GM12878-XiMat	blood
49	chr6:88184400-88193000	Weak transcription	HMEC	breast
50	chr6:88184400-88193200	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links