Variant report

Variant	rs13198879
Chromosome Location	chr6:110091064-110091065
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11964864	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11968978	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12526189	0.80[EUR][1000 genomes]
rs13191444	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13194387	0.88[EUR][1000 genomes]
rs13196280	0.91[EUR][1000 genomes]
rs13197056	0.91[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13198879	SMPD2	cis	Whole Blood	GTEx
rs13198879	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs13198879	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 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	chr6:110081200-110094200	Weak transcription	Psoas Muscle	Psoas
13	chr6:110081200-110109600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr6:110081600-110092200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr6:110081600-110115000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:110081800-110093400	Weak transcription	Hela-S3	cervix
17	chr6:110082000-110152600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr6:110082200-110119800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:110084200-110115400	Weak transcription	Small Intestine	intestine
20	chr6:110084400-110094000	Weak transcription	Stomach Mucosa	stomach
21	chr6:110084400-110094200	Weak transcription	HSMM	muscle
22	chr6:110084600-110094000	Weak transcription	Fetal Heart	heart
23	chr6:110085600-110112600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr6:110086400-110104600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:110086600-110093000	Weak transcription	HMEC	breast
26	chr6:110087200-110092800	Strong transcription	Primary T cells from cord blood	blood
27	chr6:110087600-110094000	Weak transcription	HSMMtube	muscle
28	chr6:110087600-110094200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:110087600-110094200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr6:110088400-110091400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr6:110088400-110107600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr6:110089000-110107600	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr6:110089200-110093800	Weak transcription	Left Ventricle	heart
34	chr6:110089400-110111400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr6:110089600-110091600	Weak transcription	Fetal Brain Female	brain
36	chr6:110089600-110094200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:110089600-110108000	Weak transcription	Brain Anterior Caudate	brain
38	chr6:110089600-110111400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:110089600-110115600	Weak transcription	Esophagus	oesophagus
40	chr6:110089600-110115600	Weak transcription	Gastric	stomach
41	chr6:110089800-110091400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:110089800-110092000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:110089800-110096600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr6:110089800-110107200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:110089800-110107400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr6:110089800-110115200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr6:110090000-110093000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:110090000-110093600	Enhancers	Primary B cells from cord blood	blood
49	chr6:110090000-110093800	Enhancers	GM12878-XiMat	blood
50	chr6:110090000-110094000	Weak transcription	Brain Hippocampus Middle	brain

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