Variant report

Variant	rs3743235
Chromosome Location	chr15:31515856-31515857
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:7)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31505148..31511050-chr15:31511462..31517687,6	K562	blood:

(count:7 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRPM1-1	chr15:31515674-31516347	XLOC_011413
2	lnc-TRPM1-1	chr15:31515674-31515912	XLOC_011413
3	lnc-TRPM1-1	chr15:31515674-31515912	XLOC_011413
4	lnc-TRPM1-1	chr15:31515674-31515915	XLOC_011413
5	lnc-TRPM1-1	chr15:31514978-31515915	XLOC_011413
6	lnc-TRPM1-1	chr15:31515674-31515915	ENSG00000259772.1
7	lnc-TRPM1-1	chr15:31515674-31515915	ENSG00000259772.2

No data

Variant related genes	Relation type
ENSG00000259448	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10438322	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12101670	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12437996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12438318	0.81[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap]
rs12439686	0.86[ASN][1000 genomes]
rs1370062	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16956707	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs1972825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28451043	0.81[AMR][1000 genomes]
rs28631253	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28669757	1.00[ASN][1000 genomes]
rs6493531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493532	0.93[EUR][1000 genomes]
rs7162278	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162751	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs754611	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944280	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
5	nsv1036018	chr15:31140415-31544888	Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv1052722	chr15:31261834-31609680	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv542315	chr15:31261834-31609680	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
9	nsv903838	chr15:31452911-31672128	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	esv1815415	chr15:31483843-31697213	Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
11	nsv903839	chr15:31495113-31576677	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	esv34100	chr15:31496514-31792591	Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
13	nsv977067	chr15:31509197-31523063	Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3743235	RP11-932O9.9	cis	Esophagus Muscularis	GTEx
rs3743235	GOLGA8R	cis	Heart Left Ventricle	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31508400-31516000	Weak transcription	Aorta	Aorta
2	chr15:31509600-31520600	Weak transcription	HepG2	liver
3	chr15:31510800-31520600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr15:31513200-31518000	Enhancers	Fetal Thymus	thymus
5	chr15:31513800-31517400	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr15:31514000-31516600	Enhancers	Duodenum Mucosa	Duodenum
7	chr15:31514000-31516800	Enhancers	Primary hematopoietic stem cells	blood
8	chr15:31514000-31517600	Enhancers	Primary B cells from cord blood	blood
9	chr15:31514200-31516000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr15:31514200-31516200	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr15:31514200-31516600	Enhancers	H1 Cell Line	embryonic stem cell
12	chr15:31514200-31516600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:31514200-31516600	Enhancers	Primary T cells fromperipheralblood	blood
14	chr15:31514200-31516800	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr15:31514200-31516800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr15:31514200-31517000	Enhancers	Esophagus	oesophagus
17	chr15:31514200-31517000	Enhancers	Spleen	Spleen
18	chr15:31514200-31517200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr15:31514200-31517400	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr15:31514200-31517800	Enhancers	Stomach Mucosa	stomach
21	chr15:31514400-31516000	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr15:31514400-31516000	Enhancers	Brain Angular Gyrus	brain
23	chr15:31514400-31516200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:31514400-31516200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr15:31514400-31516200	Weak transcription	Pancreas	Pancrea
26	chr15:31514400-31516600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:31514400-31517000	Enhancers	Primary T cells from cord blood	blood
28	chr15:31514600-31516200	Enhancers	Brain Substantia Nigra	brain
29	chr15:31514600-31516200	Weak transcription	Psoas Muscle	Psoas
30	chr15:31514600-31516600	Enhancers	Liver	Liver
31	chr15:31514600-31521400	Weak transcription	A549	lung
32	chr15:31514800-31516600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:31514800-31516800	Enhancers	Lung	lung
34	chr15:31515000-31516000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
35	chr15:31515000-31516400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
36	chr15:31515000-31516800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr15:31515000-31516800	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr15:31515000-31517800	Bivalent Enhancer	Fetal Muscle Leg	muscle
39	chr15:31515000-31521200	Weak transcription	Hela-S3	cervix
40	chr15:31515200-31516000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:31515200-31516000	Enhancers	Colonic Mucosa	Colon
42	chr15:31515200-31516200	Bivalent Enhancer	Placenta	Placenta
43	chr15:31515200-31516200	Enhancers	Left Ventricle	heart
44	chr15:31515200-31516600	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr15:31515200-31516800	Enhancers	Right Ventricle	heart
46	chr15:31515400-31516000	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr15:31515400-31516000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
48	chr15:31515400-31516000	Enhancers	HSMMtube	muscle
49	chr15:31515400-31516200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
50	chr15:31515400-31516200	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links