Variant report

Variant	rs13319559
Chromosome Location	chr3:119629095-119629096
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119626680..119629213-chr3:119811810..119814133,3	MCF-7	breast:
2	chr3:119628793..119630341-chr3:119631140..119633914,2	K562	blood:
3	chr3:119628367..119630716-chr3:119632308..119634691,2	MCF-7	breast:
4	chr3:119626669..119629157-chr3:119817976..119820663,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12330290	0.80[AFR][1000 genomes]
rs12330358	0.92[AFR][1000 genomes]
rs12330670	0.92[AFR][1000 genomes]
rs13315412	1.00[AFR][1000 genomes]
rs13316265	0.92[AFR][1000 genomes]
rs13319151	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs13319825	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs13323804	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs28366921	0.84[AFR][1000 genomes]
rs28481299	0.92[AFR][1000 genomes]
rs28540006	0.92[AFR][1000 genomes]
rs28709836	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs28817295	1.00[AFR][1000 genomes]
rs6769820	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs6772172	0.87[YRI][hapmap];1.00[AFR][1000 genomes]
rs6778773	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6796719	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7639665	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7639675	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9289137	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9289139	0.96[AFR][1000 genomes]
rs9810851	1.00[AFR][1000 genomes]
rs9816765	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9816864	1.00[AFR][1000 genomes]
rs9819836	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9825770	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9826355	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9831646	1.00[YRI][hapmap]
rs9835672	1.00[AFR][1000 genomes]
rs9836177	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9836325	1.00[AFR][1000 genomes]
rs9837710	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9840111	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9841959	1.00[AFR][1000 genomes]
rs9842216	1.00[AFR][1000 genomes]
rs9842542	1.00[AFR][1000 genomes]
rs9843873	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9852118	1.00[AFR][1000 genomes]
rs9852797	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9854117	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9857139	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs9857548	1.00[AFR][1000 genomes]
rs9858471	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9861481	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9862099	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9864153	1.00[AFR][1000 genomes]
rs9869296	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs9871701	1.00[AFR][1000 genomes]
rs9871925	1.00[AFR][1000 genomes]
rs9872693	1.00[AFR][1000 genomes]
rs9874110	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9880833	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9881985	1.00[YRI][hapmap];1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv829696	chr3:119567659-119711405	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119546000-119663400	Weak transcription	Lung	lung
2	chr3:119569400-119629400	Weak transcription	Esophagus	oesophagus
3	chr3:119574600-119631600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:119582400-119629400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:119583800-119630400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr3:119597600-119659000	Weak transcription	Gastric	stomach
7	chr3:119608000-119643600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:119608200-119639200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:119608200-119677800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:119608400-119629800	Weak transcription	Fetal Brain Female	brain
11	chr3:119608600-119629200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:119608600-119630000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:119608600-119630000	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:119608800-119629800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:119609000-119629600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:119609200-119630000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:119611200-119630200	Weak transcription	Psoas Muscle	Psoas
18	chr3:119611200-119643400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:119611200-119667000	Weak transcription	Pancreas	Pancrea
20	chr3:119611400-119629400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:119611400-119629400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:119611400-119630000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:119611400-119630200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:119611400-119630600	Weak transcription	Small Intestine	intestine
25	chr3:119611400-119631000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:119611400-119632200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:119611400-119632200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:119611400-119634600	Weak transcription	Spleen	Spleen
29	chr3:119611400-119642000	Weak transcription	Fetal Brain Male	brain
30	chr3:119611400-119649400	Weak transcription	Brain Hippocampus Middle	brain
31	chr3:119611400-119682200	Weak transcription	HSMMtube	muscle
32	chr3:119611600-119629600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:119613000-119637400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr3:119614200-119645200	Weak transcription	K562	blood
35	chr3:119617400-119631000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:119618200-119629600	Weak transcription	NHEK	skin
37	chr3:119618400-119631600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:119618400-119639800	Weak transcription	NHLF	lung
39	chr3:119618600-119630000	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:119620600-119635800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr3:119621200-119631000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:119621200-119631400	Strong transcription	Primary B cells from peripheral blood	blood
43	chr3:119621200-119639600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr3:119621400-119632400	Strong transcription	Primary B cells from cord blood	blood
45	chr3:119621600-119632400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:119621800-119630800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:119621800-119631000	Strong transcription	Dnd41	blood
48	chr3:119621800-119639000	Weak transcription	Fetal Intestine Small	intestine
49	chr3:119622000-119633600	Weak transcription	Colonic Mucosa	Colon
50	chr3:119622200-119640800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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