Variant report

Variant	rs12102243
Chromosome Location	chr15:35141832-35141833
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:35130591..35132648-chr15:35139707..35142491,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC114546.1-7	chr15:35141428-35141868	NONHSAT041608

Extended variants
information (count: 21 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1055356	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs11629482	0.81[ASN][1000 genomes]
rs11635293	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11637397	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12591523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12593508	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs12594365	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12911447	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1402860	0.81[CEU][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs17237170	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17237191	0.93[CEU][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2339648	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2879531	0.82[ASN][1000 genomes]
rs34185281	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3350109	chr15:34668106-35534229	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv569133	chr15:34881304-35142566	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv522411	chr15:34953986-35462981	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv457106	chr15:35049787-35227613	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv569153	chr15:35049787-35227613	Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	esv2761865	chr15:35101678-35271639	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv832967	chr15:35110102-35267906	Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12102243	TMPRSS3	trans	lymphoblastoid	seeQTL
rs12102243	BC040221	trans	multi-tissue	Pritchard
rs12102243	LOC727818	cis	Liver	GTEx
rs12102243	OR10G9	trans	multi-tissue	Pritchard
rs12102243	BC001739	cis	multi-tissue	Pritchard
rs12102243	XM_371643	trans	multi-tissue	Pritchard
rs12102243	OR10G9	cis	Liver	GTEx
rs12102243	IQCF5	cis	Liver	GTEx
rs12102243	XM_212432	trans	multi-tissue	Pritchard

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:35128800-35142400	Weak transcription	Pancreas	Pancrea
2	chr15:35129200-35147600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:35130000-35145600	Weak transcription	A549	lung
4	chr15:35130200-35147800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:35130400-35147600	Weak transcription	NHLF	lung
6	chr15:35134000-35145200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr15:35134000-35145600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr15:35134000-35147400	Weak transcription	NHDF-Ad	bronchial
9	chr15:35134600-35147600	Weak transcription	HSMM	muscle
10	chr15:35134800-35147400	Weak transcription	Fetal Muscle Leg	muscle
11	chr15:35139600-35148000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr15:35139800-35143800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:35140000-35145000	Weak transcription	Primary T cells from cord blood	blood
14	chr15:35140200-35144800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr15:35140200-35145000	Weak transcription	Hela-S3	cervix
16	chr15:35140200-35146800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:35140400-35146800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr15:35140400-35221600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr15:35140600-35148000	Weak transcription	NHEK	skin
20	chr15:35140800-35145000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:35140800-35146600	Weak transcription	Fetal Intestine Large	intestine
22	chr15:35140800-35147200	Weak transcription	Thymus	Thymus
23	chr15:35140800-35147400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr15:35141000-35146800	Weak transcription	NH-A	brain
25	chr15:35141000-35147200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr15:35141000-35148000	Weak transcription	Fetal Brain Female	brain
27	chr15:35141400-35142600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:35141400-35142600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr15:35141400-35147200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr15:35141600-35154800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr15:35141800-35142200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr15:35141800-35142400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr15:35141800-35142400	Weak transcription	Lung	lung
34	chr15:35141800-35143000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:35141800-35145000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr15:35141800-35145000	Weak transcription	Fetal Kidney	kidney
37	chr15:35141800-35146600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:35141800-35153400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links