Variant report

Variant	rs2546115
Chromosome Location	chr5:112214093-112214094
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112213045..112215334-chr5:112215360..112217961,2	K562	blood:
2	chr5:112213405..112216248-chr5:112216805..112218995,2	K562	blood:
3	chr5:112204419..112206839-chr5:112213966..112216300,2	K562	blood:
4	chr5:112197996..112200677-chr5:112212037..112214219,2	K562	blood:

Variant related genes	Relation type
ENSG00000153037	Chromatin interaction
ENSG00000272869	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1093611	0.95[CHB][hapmap];0.86[CHD][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs149193	0.81[ASN][1000 genomes]
rs153544	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs153546	0.95[CHB][hapmap];0.86[CHD][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs153548	0.95[CHB][hapmap];0.86[CHD][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs153549	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs153550	0.85[ASN][1000 genomes]
rs153551	0.89[ASN][1000 genomes]
rs153552	0.87[ASN][1000 genomes]
rs153560	0.85[CHB][hapmap];0.84[JPT][hapmap];0.81[LWK][hapmap];1.00[MKK][hapmap];0.81[ASN][1000 genomes]
rs154344	0.82[ASN][1000 genomes]
rs2229992	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs2289484	0.85[CHB][hapmap]
rs2439595	0.84[CHB][hapmap]
rs2464803	0.85[CHB][hapmap]
rs2545156	0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[ASN][1000 genomes]
rs2545170	0.88[ASN][1000 genomes]
rs2546108	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs2546110	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs2707765	0.84[CHB][hapmap]
rs3317	0.95[CHB][hapmap];0.88[CHD][hapmap];0.89[ASN][1000 genomes]
rs351767	0.85[ASN][1000 genomes]
rs351768	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs351770	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs368575	0.89[ASN][1000 genomes]
rs374613	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs382427	0.84[CHB][hapmap]
rs395858	0.82[CHB][hapmap]
rs396321	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs410701	0.88[ASN][1000 genomes]
rs414098	0.85[CHB][hapmap]
rs419155	0.95[CHB][hapmap];0.88[CHD][hapmap];0.89[ASN][1000 genomes]
rs448162	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs448613	0.89[ASN][1000 genomes]
rs454886	1.00[ASW][hapmap];0.87[CEU][hapmap];0.81[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap]
rs456531	0.92[ASN][1000 genomes]
rs459102	0.87[ASN][1000 genomes]
rs460137	0.90[CHB][hapmap]
rs467033	0.81[CHD][hapmap]
rs467660	1.00[YRI][hapmap]
rs468751	0.82[ASN][1000 genomes]
rs468854	0.80[ASN][1000 genomes]
rs469827	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs469886	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs4705624	0.84[CHB][hapmap]
rs495794	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs514763	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs566419	0.84[CHB][hapmap]
rs67293732	0.92[ASN][1000 genomes]
rs712663	0.86[ASN][1000 genomes]
rs712670	0.89[ASN][1000 genomes]
rs7213	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs818428	0.95[CHB][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs818429	0.87[ASN][1000 genomes]
rs818430	0.90[ASN][1000 genomes]
rs818797	0.95[CHB][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv870231	chr5:112192379-112247084	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1029595	chr5:112197662-112242375	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1030103	chr5:112197662-112255712	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv537863	chr5:112197662-112255712	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv4960	chr5:112200199-112218299	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2546115	FEM1C	cis	cerebellum	SCAN
rs2546115	STARD4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112198400-112220600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:112199000-112226000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:112199400-112215000	Weak transcription	Small Intestine	intestine
4	chr5:112199600-112214400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr5:112200600-112242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:112202800-112217800	Weak transcription	Brain Substantia Nigra	brain
7	chr5:112203400-112218200	Weak transcription	Colonic Mucosa	Colon
8	chr5:112203600-112214400	Weak transcription	Stomach Mucosa	stomach
9	chr5:112205000-112214600	Weak transcription	Fetal Kidney	kidney
10	chr5:112206200-112218400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:112206400-112242800	Weak transcription	Fetal Brain Male	brain
12	chr5:112206600-112214200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr5:112206600-112214400	Weak transcription	Hela-S3	cervix
14	chr5:112206600-112215400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:112206600-112215800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:112206600-112216400	Weak transcription	Aorta	Aorta
17	chr5:112206600-112217200	Weak transcription	Right Ventricle	heart
18	chr5:112206600-112219400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr5:112206600-112219800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr5:112206800-112215400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr5:112206800-112215800	Weak transcription	Pancreas	Pancrea
22	chr5:112206800-112215800	Weak transcription	Spleen	Spleen
23	chr5:112206800-112217000	Weak transcription	Brain Angular Gyrus	brain
24	chr5:112206800-112217200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr5:112206800-112217200	Weak transcription	Gastric	stomach
26	chr5:112206800-112220800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr5:112206800-112220800	Weak transcription	Ovary	ovary
28	chr5:112207000-112215800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr5:112207000-112216000	Weak transcription	Colon Smooth Muscle	Colon
30	chr5:112208200-112225800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:112209600-112214400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:112209600-112214400	Strong transcription	Fetal Thymus	thymus
33	chr5:112209600-112225000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:112209600-112226400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr5:112209600-112226800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr5:112209800-112214800	Strong transcription	Fetal Muscle Leg	muscle
37	chr5:112209800-112218600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr5:112209800-112224600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr5:112209800-112238600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:112210000-112214800	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr5:112210000-112215000	Strong transcription	Primary B cells from cord blood	blood
42	chr5:112210200-112214400	Weak transcription	Thymus	Thymus
43	chr5:112210600-112218200	Weak transcription	Psoas Muscle	Psoas
44	chr5:112210600-112225000	Strong transcription	Liver	Liver
45	chr5:112210800-112225000	Strong transcription	Duodenum Mucosa	Duodenum
46	chr5:112210800-112232400	Strong transcription	Primary B cells from peripheral blood	blood
47	chr5:112211000-112214800	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr5:112211200-112214200	Strong transcription	GM12878-XiMat	blood
49	chr5:112211200-112214400	Weak transcription	Brain Hippocampus Middle	brain
50	chr5:112211200-112216600	Strong transcription	NHDF-Ad	bronchial

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