Variant report

Variant	rs6785073
Chromosome Location	chr3:141139330-141139331
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141139030..141141005-chr3:141144023..141146849,2	MCF-7	breast:
2	chr3:141084382..141086475-chr3:141138890..141140900,2	MCF-7	breast:
3	chr3:141134135..141137819-chr3:141137972..141141592,4	K562	blood:
4	chr3:141123064..141125479-chr3:141137603..141140380,2	MCF-7	breast:
5	chr3:141138083..141140957-chr3:141173553..141175424,3	MCF-7	breast:
6	chr3:141134160..141135880-chr3:141139081..141141532,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249417	Chromatin interaction
ENSG00000177311	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs13066993	1.00[CEU][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13067032	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13068065	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13069734	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13091182	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13095453	0.92[CEU][hapmap];0.80[MEX][hapmap]
rs13099193	1.00[CEU][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2011092	1.00[CEU][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35225290	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6767786	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6767899	0.81[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6789653	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6807935	0.89[EUR][1000 genomes]
rs726838	0.92[CEU][hapmap]
rs9821337	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9822195	1.00[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9822327	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9857275	0.92[CEU][hapmap];0.80[MEX][hapmap]
rs9858603	0.82[AMR][1000 genomes];0.95[EUR][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	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6785073	RASA2	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141131600-141144400	Strong transcription	Fetal Intestine Large	intestine
2	chr3:141131600-141145200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:141131800-141144600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:141131800-141161200	Weak transcription	Thymus	Thymus
5	chr3:141132200-141141000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:141132200-141144400	Strong transcription	Fetal Intestine Small	intestine
7	chr3:141132200-141144800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:141132200-141171000	Weak transcription	Primary B cells from cord blood	blood
9	chr3:141133600-141140600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:141133800-141140400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:141133800-141140600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:141133800-141158400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:141133800-141158400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:141134000-141146800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:141134000-141161600	Weak transcription	Fetal Brain Male	brain
16	chr3:141134200-141145200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:141134200-141161600	Weak transcription	Primary T cells from cord blood	blood
18	chr3:141134400-141140600	Weak transcription	Esophagus	oesophagus
19	chr3:141134600-141144400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:141134600-141144600	Weak transcription	Liver	Liver
21	chr3:141134600-141148000	Weak transcription	Brain Germinal Matrix	brain
22	chr3:141134800-141139400	Strong transcription	Osteobl	bone
23	chr3:141134800-141142200	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr3:141135200-141144600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:141135400-141144000	Weak transcription	Fetal Kidney	kidney
26	chr3:141135600-141160200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr3:141136000-141139600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr3:141136000-141144600	Weak transcription	K562	blood
29	chr3:141136200-141140800	Weak transcription	Fetal Brain Female	brain
30	chr3:141136200-141144600	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr3:141136200-141144800	Weak transcription	Colonic Mucosa	Colon
32	chr3:141136400-141142000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:141136400-141144400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:141136400-141145000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr3:141137200-141139400	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr3:141137400-141140400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:141137400-141140600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:141137400-141140600	Weak transcription	Gastric	stomach
39	chr3:141137400-141140600	Weak transcription	Pancreas	Pancrea
40	chr3:141137400-141144400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:141137400-141144800	Weak transcription	Stomach Mucosa	stomach
42	chr3:141137600-141144400	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr3:141137600-141146400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr3:141137800-141139400	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr3:141137800-141139800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:141137800-141140200	Weak transcription	HMEC	breast
47	chr3:141137800-141140400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:141137800-141142400	Weak transcription	HepG2	liver
49	chr3:141137800-141144800	Weak transcription	HSMMtube	muscle
50	chr3:141138000-141139600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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