Variant report

Variant	rs56009458
Chromosome Location	chr6:110090077-110090078
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1096136	0.82[EUR][1000 genomes]
rs11751112	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753828	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11754263	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11757485	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11757580	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11759958	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17540056	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17612758	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17612996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56125306	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56264193	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58068940	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62437563	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62437568	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568601	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568604	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900133	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6900187	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6917300	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6924436	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6942171	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756284	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7772938	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9374121	0.86[EUR][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	nsv949475	chr6:109907936-110160501	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv5436	chr6:110052812-110097662	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv886533	chr6:110067773-110126393	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56009458	C6orf199	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
2	chr6:110035200-110094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr6:110036800-110115600	Weak transcription	Colonic Mucosa	Colon
4	chr6:110044200-110115400	Weak transcription	Brain Angular Gyrus	brain
5	chr6:110058800-110112400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr6:110059200-110124000	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:110065200-110111200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:110065400-110094200	Weak transcription	Brain Substantia Nigra	brain
9	chr6:110065800-110107400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:110065800-110107400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:110078800-110107400	Weak transcription	Fetal Brain Male	brain
12	chr6:110081000-110090800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:110081200-110094200	Weak transcription	Psoas Muscle	Psoas
14	chr6:110081200-110109600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:110081600-110090200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr6:110081600-110092200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:110081600-110115000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:110081800-110093400	Weak transcription	Hela-S3	cervix
19	chr6:110082000-110152600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr6:110082200-110119800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr6:110084000-110090200	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:110084200-110115400	Weak transcription	Small Intestine	intestine
23	chr6:110084400-110094000	Weak transcription	Stomach Mucosa	stomach
24	chr6:110084400-110094200	Weak transcription	HSMM	muscle
25	chr6:110084600-110094000	Weak transcription	Fetal Heart	heart
26	chr6:110085600-110112600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr6:110085800-110090200	Strong transcription	Liver	Liver
28	chr6:110086200-110090200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:110086400-110090200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:110086400-110104600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr6:110086600-110093000	Weak transcription	HMEC	breast
32	chr6:110086800-110090200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:110087200-110090200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:110087200-110090400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:110087200-110092800	Strong transcription	Primary T cells from cord blood	blood
36	chr6:110087400-110090200	Strong transcription	Stomach Smooth Muscle	stomach
37	chr6:110087600-110094000	Weak transcription	HSMMtube	muscle
38	chr6:110087600-110094200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:110087600-110094200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr6:110087800-110090400	Strong transcription	Fetal Thymus	thymus
41	chr6:110088400-110091400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr6:110088400-110107600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr6:110088600-110090200	Strong transcription	Fetal Muscle Leg	muscle
44	chr6:110088800-110090200	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr6:110088800-110090200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr6:110088800-110090200	Strong transcription	Fetal Intestine Small	intestine
47	chr6:110088800-110090400	Strong transcription	Fetal Intestine Large	intestine
48	chr6:110089000-110090200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:110089000-110090200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:110089000-110090200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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