Variant report

Variant	rs3800490
Chromosome Location	chr6:64372659-64372660
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:64281613..64283644-chr6:64370499..64373275,2	MCF-7	breast:
2	chr6:64366176..64368183-chr6:64370722..64372913,2	MCF-7	breast:
3	chr6:64362965..64366305-chr6:64371528..64374240,3	K562	blood:

Variant related genes	Relation type
ENSG00000266680	Chromatin interaction
ENSG00000112245	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1029091	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10943958	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10944026	0.81[ASN][1000 genomes]
rs12523702	0.81[CHD][hapmap]
rs13199206	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13199805	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13208965	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13216525	0.91[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs1412864	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1412865	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2627797	0.86[LWK][hapmap];0.81[YRI][hapmap]
rs3800489	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4351235	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4634434	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4710256	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4710257	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4710436	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4710439	0.81[ASN][1000 genomes]
rs58429651	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs756274	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs7762059	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7764184	0.85[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	nsv830674	chr6:64355412-64535801	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3800490	LGSN	cis	Whole Blood	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:64347000-64383200	Weak transcription	Esophagus	oesophagus
2	chr6:64347000-64422400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:64347600-64381000	Weak transcription	Fetal Thymus	thymus
4	chr6:64347800-64386400	Weak transcription	Colonic Mucosa	Colon
5	chr6:64350200-64374400	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr6:64350200-64381200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:64350200-64382800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr6:64350600-64373200	Weak transcription	HSMM	muscle
9	chr6:64351000-64373200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr6:64351200-64385000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:64351200-64405000	Weak transcription	Thymus	Thymus
12	chr6:64352800-64374200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr6:64354000-64421200	Weak transcription	Gastric	stomach
14	chr6:64354200-64383600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr6:64355000-64373000	Weak transcription	NH-A	brain
16	chr6:64355200-64373200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:64355200-64381600	Weak transcription	Fetal Intestine Small	intestine
18	chr6:64357400-64381200	Weak transcription	Dnd41	blood
19	chr6:64357600-64373000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:64357800-64393400	Weak transcription	Placenta	Placenta
21	chr6:64358400-64382800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:64360000-64373200	Weak transcription	NHDF-Ad	bronchial
23	chr6:64360200-64372800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:64360200-64373200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:64360200-64373200	Weak transcription	Adipose Nuclei	Adipose
26	chr6:64363000-64374600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr6:64363200-64382800	Weak transcription	Fetal Muscle Leg	muscle
28	chr6:64365000-64373600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:64365200-64387000	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr6:64365400-64373200	Weak transcription	Right Ventricle	heart
31	chr6:64365400-64374400	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr6:64365400-64386400	Weak transcription	Spleen	Spleen
33	chr6:64365600-64374400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr6:64365800-64375400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr6:64365800-64375400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:64365800-64409400	Weak transcription	Fetal Stomach	stomach
37	chr6:64366000-64374600	Weak transcription	Primary B cells from cord blood	blood
38	chr6:64366600-64373200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:64366600-64382400	Weak transcription	Fetal Lung	lung
40	chr6:64367000-64373400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr6:64367600-64372800	Weak transcription	Small Intestine	intestine
42	chr6:64368000-64380600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:64368000-64381800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:64368800-64374000	Weak transcription	GM12878-XiMat	blood
45	chr6:64370200-64373800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr6:64370600-64374400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr6:64370800-64378000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr6:64370800-64383000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr6:64370800-64383400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr6:64370800-64395000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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