Variant report

Variant	rs13323804
Chromosome Location	chr3:119721577-119721578
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	chr3:119721357..119723738-chr3:119814057..119815870,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 56 )
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]
rs13319559	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs13319825	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:3 , 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	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
3	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:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119681200-119723200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:119689000-119722600	Weak transcription	Gastric	stomach
3	chr3:119692400-119723200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr3:119693600-119732200	Weak transcription	A549	lung
5	chr3:119700600-119722800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:119701000-119722600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:119709000-119722600	Weak transcription	Ovary	ovary
8	chr3:119709200-119723000	Weak transcription	Spleen	Spleen
9	chr3:119710200-119722600	Weak transcription	Stomach Mucosa	stomach
10	chr3:119710200-119730800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:119710400-119722800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:119711400-119729200	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:119711800-119722800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:119711800-119723200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr3:119712000-119723400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr3:119712000-119732200	Weak transcription	HepG2	liver
17	chr3:119712200-119723400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:119712200-119732400	Weak transcription	NHLF	lung
19	chr3:119712400-119722800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:119712600-119745000	Weak transcription	Hela-S3	cervix
21	chr3:119712800-119722000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:119712800-119722800	Weak transcription	Thymus	Thymus
23	chr3:119712800-119723400	Weak transcription	Osteobl	bone
24	chr3:119712800-119732200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr3:119713000-119722000	Weak transcription	Psoas Muscle	Psoas
26	chr3:119713000-119722800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:119713200-119744400	Weak transcription	Fetal Kidney	kidney
28	chr3:119713800-119722600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr3:119714400-119722600	Weak transcription	Brain Angular Gyrus	brain
30	chr3:119714400-119723000	Weak transcription	Fetal Brain Male	brain
31	chr3:119715600-119722800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:119715800-119722600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:119716400-119722000	Weak transcription	K562	blood
34	chr3:119716400-119722600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:119716800-119722000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:119717000-119722800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:119717400-119721800	Weak transcription	Aorta	Aorta
38	chr3:119717400-119722000	Weak transcription	Small Intestine	intestine
39	chr3:119717400-119722600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:119717400-119722600	Weak transcription	Left Ventricle	heart
41	chr3:119717400-119722600	Weak transcription	Pancreas	Pancrea
42	chr3:119717400-119722800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:119717400-119722800	Weak transcription	Lung	lung
44	chr3:119717400-119722800	Weak transcription	Right Ventricle	heart
45	chr3:119717400-119730200	Weak transcription	Brain Anterior Caudate	brain
46	chr3:119717600-119722600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr3:119717600-119722600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:119717600-119722600	Weak transcription	Fetal Intestine Large	intestine
49	chr3:119717600-119722800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:119717600-119722800	Weak transcription	Fetal Intestine Small	intestine

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