Variant report

Variant	rs13343573
Chromosome Location	chr19:39426826-39426827
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39421479..39423080-chr19:39424950..39427056,2	MCF-7	breast:
2	chr19:39338909..39344654-chr19:39419169..39426961,19	MCF-7	breast:
3	chr19:39424291..39427165-chr19:39431184..39433812,2	K562	blood:

Variant related genes	Relation type
ENSG00000128626	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000104835	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10411209	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10411301	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10423309	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11083487	1.00[ASN][1000 genomes]
rs12977453	1.00[ASN][1000 genomes]
rs16972885	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17883664	1.00[ASN][1000 genomes]
rs2070250	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2070251	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2082436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2116853	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2163811	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2304115	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2304116	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28808414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28824318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28844707	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28860185	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34264048	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45535036	1.00[ASN][1000 genomes]
rs59849895	1.00[ASN][1000 genomes]
rs61194027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61232096	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61347610	1.00[ASN][1000 genomes]
rs6508826	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508827	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73537681	1.00[ASN][1000 genomes]
rs73930228	0.84[AMR][1000 genomes]
rs73930229	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs8113749	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39422400-39434600	Weak transcription	Fetal Kidney	kidney
2	chr19:39422400-39435000	Weak transcription	Fetal Lung	lung
3	chr19:39422400-39435000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:39422400-39440600	Weak transcription	NHDF-Ad	bronchial
5	chr19:39422600-39427000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr19:39422600-39430200	Weak transcription	HUVEC	blood vessel
7	chr19:39422600-39430800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr19:39422600-39435200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr19:39422600-39435200	Weak transcription	HSMM	muscle
10	chr19:39422600-39440200	Weak transcription	NH-A	brain
11	chr19:39422600-39440600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr19:39422600-39453000	Weak transcription	HSMMtube	muscle
13	chr19:39422800-39432600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:39423200-39440800	Weak transcription	Fetal Heart	heart
15	chr19:39423400-39436800	Weak transcription	Aorta	Aorta
16	chr19:39423600-39432400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:39423600-39433400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr19:39423600-39435000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr19:39423600-39440400	Weak transcription	Right Atrium	heart
20	chr19:39423600-39440600	Weak transcription	Gastric	stomach
21	chr19:39424000-39435200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr19:39424200-39435400	Weak transcription	NHLF	lung
23	chr19:39424400-39432000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:39424400-39435000	Weak transcription	Adipose Nuclei	Adipose
25	chr19:39424400-39436800	Weak transcription	Brain Angular Gyrus	brain
26	chr19:39424400-39440000	Weak transcription	Fetal Brain Female	brain
27	chr19:39424600-39427800	Weak transcription	Small Intestine	intestine
28	chr19:39424600-39434400	Weak transcription	Fetal Intestine Large	intestine
29	chr19:39424600-39434600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr19:39424600-39434600	Weak transcription	Colon Smooth Muscle	Colon
31	chr19:39424600-39436600	Weak transcription	Brain Anterior Caudate	brain
32	chr19:39424600-39440200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr19:39424600-39440200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:39424800-39440200	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr19:39424800-39440200	Weak transcription	Brain Substantia Nigra	brain
36	chr19:39425000-39427400	Enhancers	Liver	Liver
37	chr19:39425200-39427000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr19:39425400-39436800	Weak transcription	Lung	lung
39	chr19:39425400-39440400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:39425600-39428200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:39425600-39429000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr19:39425600-39431800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr19:39425600-39434400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:39425600-39434400	Weak transcription	Ovary	ovary
45	chr19:39425600-39434600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr19:39425600-39436800	Weak transcription	Brain Hippocampus Middle	brain
47	chr19:39425600-39440200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr19:39425800-39427800	Weak transcription	Primary B cells from cord blood	blood
49	chr19:39425800-39427800	Weak transcription	Primary T cells from cord blood	blood
50	chr19:39425800-39427800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links