Variant report

Variant	rs10943958
Chromosome Location	chr6:64414912-64414913
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:64281048..64283887-chr6:64413696..64416630,3	K562	blood:
2	chr6:64344714..64347483-chr6:64412709..64415524,2	K562	blood:
3	chr6:64345547..64349156-chr6:64414533..64419389,4	K562	blood:

Variant related genes	Relation type
ENSG00000266680	Chromatin interaction
ENSG00000112245	Chromatin interaction
ENSG00000118482	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1029091	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10944026	0.85[ASN][1000 genomes]
rs13197043	0.87[ASN][1000 genomes]
rs13199206	0.86[ASN][1000 genomes]
rs13199805	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13208965	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13216525	0.83[ASN][1000 genomes]
rs1412864	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1412865	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3800489	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3800490	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4351235	0.82[EUR][1000 genomes]
rs4634434	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4710256	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4710257	0.88[ASN][1000 genomes]
rs4710436	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4710439	0.85[ASN][1000 genomes]
rs58429651	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs756274	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7764184	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv1022376	chr6:64386826-64445195	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10943958	LGSN	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:64347000-64422400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:64354000-64421200	Weak transcription	Gastric	stomach
3	chr6:64387200-64421000	Weak transcription	Aorta	Aorta
4	chr6:64387400-64419400	Weak transcription	Fetal Heart	heart
5	chr6:64387600-64421000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:64387600-64423400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:64390000-64417600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr6:64392200-64422400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:64392800-64425200	Weak transcription	NHEK	skin
10	chr6:64393200-64417600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:64393400-64423400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr6:64395400-64420200	Weak transcription	Fetal Brain Male	brain
13	chr6:64395800-64420200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:64397400-64422400	Weak transcription	Pancreas	Pancrea
15	chr6:64399200-64418600	Weak transcription	A549	lung
16	chr6:64401000-64426400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:64402000-64419200	Weak transcription	Brain Substantia Nigra	brain
18	chr6:64404000-64424600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr6:64404200-64417400	Strong transcription	Fetal Lung	lung
20	chr6:64404200-64423600	Strong transcription	Dnd41	blood
21	chr6:64404200-64423800	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr6:64404200-64424200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr6:64404200-64424600	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr6:64404200-64424600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:64404200-64426600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:64404400-64417600	Strong transcription	HepG2	liver
27	chr6:64404400-64424200	Strong transcription	Fetal Thymus	thymus
28	chr6:64404400-64424800	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr6:64404400-64425000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:64404400-64426800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:64404800-64420600	Weak transcription	Small Intestine	intestine
32	chr6:64404800-64424200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:64404800-64424200	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr6:64404800-64425000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr6:64405000-64417600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:64405000-64417600	Strong transcription	Primary B cells from cord blood	blood
37	chr6:64405000-64424200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:64405400-64426400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:64405600-64422200	Weak transcription	Right Ventricle	heart
40	chr6:64406000-64426400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:64406200-64424200	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr6:64406400-64423600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr6:64406600-64420600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:64406600-64423600	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr6:64407200-64419000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:64407800-64422400	Weak transcription	Spleen	Spleen
47	chr6:64408000-64416800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:64408000-64423800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:64408200-64423600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr6:64408200-64425200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links