Variant report

Variant	rs4795408
Chromosome Location	chr17:38107627-38107628
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38101089..38105078-chr17:38105781..38110100,7	K562	blood:
2	chr17:38102879..38104734-chr17:38106799..38109127,2	MCF-7	breast:
3	chr17:38091500..38094423-chr17:38107517..38109034,2	MCF-7	breast:
4	chr17:38107392..38113362-chr17:38135377..38138663,7	K562	blood:
5	chr17:38097357..38100615-chr17:38107229..38110087,5	K562	blood:
6	chr17:38107027..38109287-chr17:38138129..38139921,2	K562	blood:

Variant related genes	Relation type
ENSG00000204913	Chromatin interaction
ENSG00000108344	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12451084	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12451100	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12601749	0.85[ASN][1000 genomes]
rs12603481	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35123741	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3893044	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs3894194	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3902025	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs4065985	0.86[ASN][1000 genomes]
rs4065986	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4795406	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4795409	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55739615	0.92[ASN][1000 genomes]
rs56199421	0.85[ASN][1000 genomes]
rs62068170	0.91[ASN][1000 genomes]
rs62068171	0.92[ASN][1000 genomes]
rs6503525	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6503526	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7212938	0.81[CEU][hapmap]
rs7216564	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8069202	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8079416	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs8080734	0.92[ASN][1000 genomes]
rs8081462	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[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	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4795408	GSDMA	cis	Nerve Tibial	GTEx
rs4795408	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs4795408	GSDMA	cis	Esophagus Muscularis	GTEx
rs4795408	GSDMA	cis	Artery Aorta	GTEx
rs4795408	GSDMA	cis	Adipose Subcutaneous	GTEx
rs4795408	GSDMA	cis	Thyroid	GTEx
rs4795408	GSDMA	cis	Artery Tibial	GTEx
rs4795408	GSDMB	cis	Whole Blood	GTEx
rs4795408	GSDMA	cis	lung	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38096400-38108400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr17:38100800-38108400	Weak transcription	Esophagus	oesophagus
3	chr17:38103200-38108400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr17:38103600-38108200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr17:38103600-38108600	Weak transcription	HMEC	breast
6	chr17:38104400-38108400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr17:38105200-38108400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr17:38105200-38108400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr17:38105200-38108400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr17:38105200-38108600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr17:38105400-38108200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr17:38105400-38108200	Weak transcription	Stomach Mucosa	stomach
13	chr17:38105400-38108400	Weak transcription	Primary T cells from cord blood	blood
14	chr17:38105400-38108400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr17:38105400-38108400	Weak transcription	Fetal Lung	lung
16	chr17:38105400-38108600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr17:38105400-38108600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr17:38105400-38108600	Weak transcription	Thymus	Thymus
19	chr17:38105400-38108600	Weak transcription	A549	lung
20	chr17:38105600-38108200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr17:38105600-38108400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr17:38105600-38108400	Weak transcription	Fetal Intestine Large	intestine
23	chr17:38105600-38108400	Weak transcription	Fetal Intestine Small	intestine
24	chr17:38105800-38108200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr17:38105800-38108600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr17:38106200-38108600	Enhancers	Liver	Liver
27	chr17:38106400-38108600	Enhancers	Fetal Muscle Leg	muscle
28	chr17:38106600-38108200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr17:38106600-38108600	Enhancers	Fetal Muscle Trunk	muscle
30	chr17:38106800-38107800	Enhancers	Pancreas	Pancrea
31	chr17:38107000-38107800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr17:38107000-38108000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr17:38107000-38108400	Weak transcription	Left Ventricle	heart
34	chr17:38107000-38108400	Weak transcription	Right Atrium	heart
35	chr17:38107000-38108400	Weak transcription	Right Ventricle	heart
36	chr17:38107000-38108400	Weak transcription	Spleen	Spleen
37	chr17:38107000-38108600	Enhancers	Primary B cells from cord blood	blood
38	chr17:38107200-38108200	Weak transcription	K562	blood
39	chr17:38107200-38108400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr17:38107200-38108400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr17:38107400-38107800	Enhancers	Lung	lung
42	chr17:38107400-38108200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr17:38107400-38108200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr17:38107400-38108400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr17:38107400-38108400	Weak transcription	Adipose Nuclei	Adipose
46	chr17:38107400-38108400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr17:38107400-38108600	Enhancers	Placenta	Placenta
48	chr17:38107600-38108000	Weak transcription	Fetal Thymus	thymus
49	chr17:38107600-38108200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr17:38107600-38108200	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links