Variant report

Variant	rs4710256
Chromosome Location	chr6:64368449-64368450
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:64363425..64368282-chr6:64368338..64371068,4	K562	blood:
2	chr6:64357764..64359971-chr6:64365993..64369185,4	K562	blood:
3	chr6:64366148..64368901-chr6:64374684..64376667,2	MCF-7	breast:
4	chr6:64352758..64355671-chr6:64367534..64370058,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs1029091	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10943958	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12523702	0.86[CHD][hapmap]
rs13199206	0.84[EUR][1000 genomes]
rs13199805	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13208965	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13216525	0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs1412864	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1412865	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3800489	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3800490	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4351235	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4634434	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4710257	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4710436	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58429651	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[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	0.83[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
rs4710256	LGSN	cis	Whole Blood	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:64347000-64370600	Weak transcription	Left Ventricle	heart
2	chr6:64347000-64383200	Weak transcription	Esophagus	oesophagus
3	chr6:64347000-64422400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:64347400-64370800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr6:64347600-64381000	Weak transcription	Fetal Thymus	thymus
6	chr6:64347800-64370600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:64347800-64386400	Weak transcription	Colonic Mucosa	Colon
8	chr6:64349400-64370600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:64350200-64374400	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr6:64350200-64381200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:64350200-64382800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr6:64350400-64369600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr6:64350600-64373200	Weak transcription	HSMM	muscle
14	chr6:64351000-64373200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:64351200-64385000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:64351200-64405000	Weak transcription	Thymus	Thymus
17	chr6:64351400-64369400	Weak transcription	Fetal Heart	heart
18	chr6:64352800-64374200	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr6:64354000-64421200	Weak transcription	Gastric	stomach
20	chr6:64354200-64383600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr6:64355000-64373000	Weak transcription	NH-A	brain
22	chr6:64355200-64373200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:64355200-64381600	Weak transcription	Fetal Intestine Small	intestine
24	chr6:64357200-64370600	Weak transcription	Psoas Muscle	Psoas
25	chr6:64357400-64381200	Weak transcription	Dnd41	blood
26	chr6:64357600-64373000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:64357800-64393400	Weak transcription	Placenta	Placenta
28	chr6:64358400-64369600	Weak transcription	HepG2	liver
29	chr6:64358400-64370000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr6:64358400-64382800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr6:64359800-64370000	Weak transcription	K562	blood
32	chr6:64359800-64370600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:64359800-64372600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:64360000-64371400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr6:64360000-64373200	Weak transcription	NHDF-Ad	bronchial
36	chr6:64360200-64372800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:64360200-64373200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:64360200-64373200	Weak transcription	Adipose Nuclei	Adipose
39	chr6:64360600-64370600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr6:64360800-64369400	Weak transcription	Brain Angular Gyrus	brain
41	chr6:64361200-64369400	Weak transcription	Brain Substantia Nigra	brain
42	chr6:64361600-64370600	Weak transcription	Pancreas	Pancrea
43	chr6:64361800-64369600	Weak transcription	Brain Hippocampus Middle	brain
44	chr6:64362600-64371200	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr6:64362800-64369600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:64362800-64370000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr6:64362800-64371800	Enhancers	Primary T cells from cord blood	blood
48	chr6:64363000-64374600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr6:64363200-64382800	Weak transcription	Fetal Muscle Leg	muscle
50	chr6:64363800-64372400	Weak transcription	Hela-S3	cervix

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