Variant report

Variant	rs3935281
Chromosome Location	chr17:38188419-38188420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:38188226-38188630	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38186956..38189285-chr17:38277209..38280047,2	MCF-7	breast:

Variant related genes	Relation type
MED24	TF binding region
SNORD124	TF binding region
ENSG00000188895	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10445310	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11078930	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11078931	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11078935	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11078936	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11654208	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11655264	0.83[ASN][1000 genomes]
rs11655655	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11658328	0.85[ASN][1000 genomes]
rs11867302	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12309	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12450800	0.81[ASN][1000 genomes]
rs12451547	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12451897	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12453334	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12453341	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12453343	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12453764	0.83[ASN][1000 genomes]
rs12601929	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12602514	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12602854	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12939682	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12940405	0.83[ASN][1000 genomes]
rs2227319	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2227321	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2227333	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241244	0.85[ASN][1000 genomes]
rs2241245	0.85[ASN][1000 genomes]
rs2270401	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2302774	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2302777	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2305481	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2305482	0.82[ASN][1000 genomes]
rs25645	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3087852	0.83[ASN][1000 genomes]
rs34003767	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34342173	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34453912	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34540281	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34648856	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34933056	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35272691	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35982947	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36071767	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3744245	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3785550	0.82[ASN][1000 genomes]
rs3816472	0.85[ASN][1000 genomes]
rs3859187	0.85[ASN][1000 genomes]
rs3859189	0.83[ASN][1000 genomes]
rs4065321	0.85[ASN][1000 genomes]
rs4072639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4433838	0.85[ASN][1000 genomes]
rs66826786	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7502971	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8066582	0.85[ASN][1000 genomes]
rs8070444	0.85[ASN][1000 genomes]
rs8071037	0.85[ASN][1000 genomes]
rs8073254	0.85[ASN][1000 genomes]
rs8075668	0.83[ASN][1000 genomes]
rs9898547	0.82[ASN][1000 genomes]
rs9915252	0.85[ASN][1000 genomes]
rs9916158	0.91[EUR][1000 genomes];0.92[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3935281	GSDMA	cis	Esophagus Muscularis	GTEx
rs3935281	MED24	cis	Muscle Skeletal	GTEx
rs3935281	GSDMA	cis	Adipose Subcutaneous	GTEx
rs3935281	MED24	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38173400-38192800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:38174000-38192600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr17:38174000-38193800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr17:38174400-38193200	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr17:38174800-38192600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr17:38175000-38193800	Strong transcription	HepG2	liver
7	chr17:38175200-38192600	Strong transcription	Fetal Brain Female	brain
8	chr17:38175200-38193200	Strong transcription	Dnd41	blood
9	chr17:38175600-38191400	Strong transcription	Brain Hippocampus Middle	brain
10	chr17:38175600-38193200	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr17:38175600-38193200	Strong transcription	Brain Cingulate Gyrus	brain
12	chr17:38175600-38193800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:38175800-38192600	Strong transcription	Brain Germinal Matrix	brain
14	chr17:38176000-38189800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr17:38176000-38192600	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr17:38176000-38195400	Weak transcription	Right Atrium	heart
17	chr17:38176200-38193800	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr17:38176400-38192400	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr17:38177800-38191000	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr17:38178200-38192600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr17:38178600-38191200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr17:38179000-38192600	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr17:38180400-38191200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr17:38180400-38192600	Strong transcription	Fetal Intestine Large	intestine
25	chr17:38180400-38193800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr17:38181000-38192600	Strong transcription	Primary hematopoietic stem cells	blood
27	chr17:38181400-38192600	Strong transcription	Fetal Lung	lung
28	chr17:38181400-38193200	Strong transcription	Brain Substantia Nigra	brain
29	chr17:38181400-38193400	Strong transcription	Brain Anterior Caudate	brain
30	chr17:38181800-38192600	Strong transcription	Osteobl	bone
31	chr17:38182800-38193800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr17:38183000-38188800	Weak transcription	Fetal Brain Male	brain
33	chr17:38183000-38195600	Strong transcription	Primary T cells from cord blood	blood
34	chr17:38183200-38193800	Strong transcription	Thymus	Thymus
35	chr17:38183400-38190800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr17:38183400-38191000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr17:38183400-38192400	Strong transcription	Adipose Nuclei	Adipose
38	chr17:38183400-38192600	Strong transcription	NHLF	lung
39	chr17:38183400-38193200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr17:38183600-38188800	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr17:38183600-38189600	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr17:38183600-38191400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr17:38183600-38191600	Strong transcription	A549	lung
44	chr17:38183600-38192200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr17:38183600-38192200	Strong transcription	Esophagus	oesophagus
46	chr17:38183600-38192600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr17:38183600-38192800	Strong transcription	Fetal Intestine Small	intestine
48	chr17:38183600-38193200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr17:38183600-38193400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr17:38183600-38193800	Strong transcription	Brain Inferior Temporal Lobe	brain

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