Variant report

Variant	rs3736054
Chromosome Location	chr15:43322113-43322114
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1037990	0.81[ASN][1000 genomes]
rs11070380	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs11070382	0.93[ASW][hapmap];0.81[GIH][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap]
rs11070386	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11070387	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11070388	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11630595	1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12050596	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12592725	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap]
rs12899266	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs12913617	0.85[AMR][1000 genomes]
rs1381856	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1462856	1.00[ASW][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs16957244	0.92[ASW][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap]
rs16957250	0.82[MEX][hapmap]
rs16957264	0.82[MEX][hapmap]
rs16957385	0.83[AMR][1000 genomes]
rs1996675	0.83[AMR][1000 genomes]
rs2035170	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2054389	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2126602	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2412752	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs2682073	0.86[ASW][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap]
rs28585036	0.93[JPT][hapmap]
rs2899069	0.93[AFR][1000 genomes]
rs2947019	0.80[JPT][hapmap]
rs3784265	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3803341	0.81[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs4244590	0.85[ASN][1000 genomes]
rs4573908	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4923955	0.85[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes]
rs4924701	0.90[AFR][1000 genomes]
rs4924704	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs495286	0.80[JPT][hapmap]
rs497138	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs530305	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap]
rs531850	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs538218	0.83[CHB][hapmap]
rs6493076	1.00[ASW][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6493077	0.85[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7174028	0.93[ASW][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.95[YRI][hapmap]
rs7176116	0.87[ASN][1000 genomes]
rs7178567	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs8027371	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs8027733	0.81[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8031767	0.93[ASW][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.85[YRI][hapmap]
rs8035894	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs8036710	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8037022	0.81[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs8042481	0.82[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs9920498	0.87[AFR][1000 genomes]
rs9920904	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv904134	chr15:43097652-43357406	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv515876	chr15:43116906-43445305	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv904135	chr15:43143998-43392075	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv569239	chr15:43201109-43392075	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv569240	chr15:43201109-43445305	Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv1039587	chr15:43204351-43378274	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv569242	chr15:43210030-43445305	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv1050987	chr15:43237103-43385515	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv542369	chr15:43237103-43385515	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv904136	chr15:43257475-43482127	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
14	nsv904137	chr15:43268970-43392075	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv904138	chr15:43268970-43414673	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv904139	chr15:43268970-43482127	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
17	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
18	nsv904140	chr15:43276345-43385147	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	nsv904141	chr15:43276345-43392075	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
20	nsv904142	chr15:43276345-43403955	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
21	nsv904143	chr15:43276345-43414673	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
22	nsv904144	chr15:43276345-43482127	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
23	esv3384283	chr15:43280479-43380788	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
24	nsv904145	chr15:43286746-43392075	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
25	nsv904146	chr15:43294218-43414673	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
26	nsv1048937	chr15:43299522-43357631	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
27	nsv904147	chr15:43309429-43403955	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3736054	CCNDBP1	cis	multi-tissue	Pritchard
rs3736054	ELL3	cis	cerebellum	SCAN
rs3736054	CCNDBP1	Cis_1M	lymphoblastoid	RTeQTL
rs3736054	ELL3	cis	lymphoblastoid	seeQTL
rs3736054	TGM5	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43232000-43362800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:43267200-43323000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:43269200-43397200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:43269800-43335200	Weak transcription	Small Intestine	intestine
5	chr15:43287400-43346000	Weak transcription	A549	lung
6	chr15:43297400-43348000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:43298600-43346200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:43298800-43346000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:43299400-43346000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr15:43301800-43343800	Weak transcription	Psoas Muscle	Psoas
11	chr15:43301800-43345800	Weak transcription	Colonic Mucosa	Colon
12	chr15:43301800-43345800	Weak transcription	Pancreas	Pancrea
13	chr15:43301800-43385800	Weak transcription	Gastric	stomach
14	chr15:43303400-43345800	Weak transcription	Aorta	Aorta
15	chr15:43303400-43397400	Weak transcription	Esophagus	oesophagus
16	chr15:43306800-43331000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:43307200-43331000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:43307600-43331600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:43307800-43323400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr15:43307800-43325400	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr15:43307800-43325600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:43307800-43330600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:43307800-43330800	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr15:43308200-43327200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:43309000-43330200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:43310600-43325200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr15:43311400-43330600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:43312000-43323200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr15:43312000-43323200	Strong transcription	HSMM	muscle
30	chr15:43312000-43323400	Strong transcription	Fetal Thymus	thymus
31	chr15:43312000-43323600	Strong transcription	Dnd41	blood
32	chr15:43312000-43325200	Strong transcription	Duodenum Mucosa	Duodenum
33	chr15:43312000-43331000	Strong transcription	Adipose Nuclei	Adipose
34	chr15:43312200-43324600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr15:43312200-43325200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr15:43312200-43325200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr15:43312200-43325200	Strong transcription	Liver	Liver
38	chr15:43312200-43325200	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr15:43312200-43330600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:43312400-43323600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:43312400-43324600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr15:43312600-43323000	Strong transcription	Primary hematopoietic stem cells	blood
43	chr15:43312600-43330200	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr15:43312600-43330600	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr15:43313200-43333600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr15:43313200-43334400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr15:43313200-43339400	Weak transcription	Right Ventricle	heart
48	chr15:43313400-43334400	Weak transcription	Brain Substantia Nigra	brain
49	chr15:43315000-43322200	Weak transcription	HepG2	liver
50	chr15:43315800-43325200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links