Variant report

Variant	rs28364475
Chromosome Location	chr15:42692393-42692394
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42691473..42693889-chr15:42699891..42701622,2	K562	blood:
2	chr15:42692136..42694118-chr15:42750435..42753358,2	K562	blood:

Variant related genes	Relation type
ENSG00000092529	Chromatin interaction

Extended variants
information (count: 169 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:162)

rs_ID	r²[population]
rs10518757	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11070363	0.82[CHB][hapmap];1.00[GIH][hapmap]
rs11070367	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs11070368	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11070369	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11070371	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs11631756	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11631823	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11631922	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11635876	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11637010	1.00[JPT][hapmap]
rs11856797	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11856807	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12324205	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12441027	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12902924	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12907489	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12915946	0.82[CHB][hapmap]
rs12916523	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12916792	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12917071	0.82[CHB][hapmap]
rs1616957	0.82[CHB][hapmap]
rs1630294	0.82[CHB][hapmap];1.00[GIH][hapmap]
rs1659214	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1659215	0.82[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap]
rs1659216	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1659220	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap]
rs1659221	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1659223	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1659224	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1659226	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1678988	0.82[CHB][hapmap];1.00[GIH][hapmap]
rs1678989	0.82[CHB][hapmap]
rs1678995	0.82[CHB][hapmap]
rs1678998	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs1678999	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1679011	0.82[CHB][hapmap]
rs16972896	1.00[CEU][hapmap]
rs1703748	0.82[CHB][hapmap];1.00[GIH][hapmap]
rs1712397	0.82[CHB][hapmap]
rs1712408	0.82[CHB][hapmap]
rs1712409	0.82[CHB][hapmap]
rs1712417	0.82[CHB][hapmap];1.00[GIH][hapmap]
rs1712420	0.82[CHB][hapmap]
rs1712442	0.82[CHB][hapmap];0.94[GIH][hapmap]
rs2289293	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2289297	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2412681	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2412684	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2412686	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2412689	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2412690	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2412691	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2412694	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2412697	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2412702	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2578651	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2620375	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2620383	0.82[CHB][hapmap]
rs2620387	0.82[CHB][hapmap];0.87[GIH][hapmap]
rs2663096	0.82[CHB][hapmap]
rs28364400	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs28364462	0.81[ASW][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap]
rs28364491	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28364495	0.80[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[MKK][hapmap]
rs28364500	1.00[ASN][1000 genomes]
rs28364503	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28364504	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap]
rs28364507	0.97[ASN][1000 genomes]
rs28364508	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap]
rs28364509	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap]
rs28364511	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap]
rs28364519	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap]
rs28364526	0.96[AFR][1000 genomes]
rs28364536	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs28364540	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs28364541	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs28364544	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs28364559	1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap]
rs28489155	0.82[ASN][1000 genomes]
rs28745879	1.00[ASN][1000 genomes]
rs2899044	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2899058	1.00[GIH][hapmap]
rs2918458	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3736096	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3736097	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3743002	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3743003	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3803342	1.00[CHB][hapmap]
rs4244589	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4556762	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs4583208	0.82[CHB][hapmap]
rs4923934	0.82[CHB][hapmap]
rs4923935	0.82[CHB][hapmap]
rs4923936	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4923937	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4923938	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4923939	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs4923941	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs4924633	0.82[CHB][hapmap];1.00[GIH][hapmap]
rs4924636	0.82[CHB][hapmap];1.00[GIH][hapmap]
rs4924638	0.82[CHB][hapmap]
rs4924641	1.00[JPT][hapmap]
rs4924642	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs4924643	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4924650	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs4924651	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4924652	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4924657	1.00[CHB][hapmap]
rs4924662	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4924663	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4924664	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4924665	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4924666	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4924667	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4924668	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs4924669	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs4924670	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4924671	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs5029919	1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs602270	0.82[CHB][hapmap]
rs607959	0.82[CHB][hapmap]
rs613090	0.82[CHB][hapmap];1.00[GIH][hapmap]
rs613157	0.82[CHB][hapmap]
rs615023	0.82[CHB][hapmap];1.00[GIH][hapmap]
rs629255	0.82[CHB][hapmap]
rs637445	0.82[CHB][hapmap]
rs638240	0.82[CHB][hapmap];1.00[GIH][hapmap]
rs645304	0.82[CHB][hapmap]
rs648720	0.82[CHB][hapmap]
rs6493026	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6493034	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6493041	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs652192	0.82[CHB][hapmap]
rs659354	0.82[CHB][hapmap]
rs683227	0.82[CHB][hapmap]
rs683579	0.82[CHB][hapmap]
rs7161982	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7163941	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7167306	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7168121	0.88[GIH][hapmap]
rs7169279	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7169553	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7170943	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs7173358	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7177193	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7182963	1.00[JPT][hapmap]
rs7183399	0.94[ASN][1000 genomes]
rs7183843	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8023568	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs8023678	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs8023714	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8024390	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8025364	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8030650	0.82[CHB][hapmap]
rs8031735	0.82[CHB][hapmap];0.87[GIH][hapmap]
rs8037100	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs8037627	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs8043033	0.88[ASN][1000 genomes]
rs8043515	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8108	0.82[CHB][hapmap];1.00[GIH][hapmap]
rs9920851	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[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	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv832986	chr15:42587825-42753664	Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv832987	chr15:42627447-42792348	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv932995	chr15:42640015-42704121	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3334708	chr15:42664344-42827738	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic 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 miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42656800-42693400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr15:42656800-42697800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:42674000-42694400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr15:42675200-42702800	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:42676800-42693200	Weak transcription	Fetal Stomach	stomach
6	chr15:42677000-42693400	Weak transcription	GM12878-XiMat	blood
7	chr15:42678600-42706800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:42678800-42694000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:42678800-42702800	Weak transcription	NHLF	lung
10	chr15:42679000-42706800	Weak transcription	Right Atrium	heart
11	chr15:42679200-42694000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:42680000-42693200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:42680200-42694000	Weak transcription	Left Ventricle	heart
14	chr15:42680200-42696400	Weak transcription	HSMMtube	muscle
15	chr15:42680600-42693600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr15:42681600-42695400	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr15:42681800-42694600	Strong transcription	Skeletal Muscle Male	skeletal muscle
18	chr15:42683800-42704600	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr15:42685000-42693800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:42685200-42693600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr15:42686200-42694200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr15:42688200-42693800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:42688400-42693400	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr15:42688800-42694400	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr15:42689000-42697800	Weak transcription	NHEK	skin
26	chr15:42689000-42712400	Weak transcription	Fetal Brain Male	brain
27	chr15:42689200-42693800	Weak transcription	Colonic Mucosa	Colon
28	chr15:42689400-42693200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr15:42689400-42693800	Weak transcription	Esophagus	oesophagus
30	chr15:42689400-42696800	Weak transcription	Psoas Muscle	Psoas
31	chr15:42689400-42703200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr15:42689600-42693800	Weak transcription	Right Ventricle	heart
33	chr15:42689800-42706600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr15:42690000-42693800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:42690200-42695600	Strong transcription	Fetal Intestine Small	intestine
36	chr15:42690800-42702400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:42691000-42703000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:42691200-42692600	Strong transcription	Lung	lung
39	chr15:42691200-42692600	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr15:42691200-42692800	Strong transcription	Spleen	Spleen
41	chr15:42691200-42696000	Strong transcription	Fetal Muscle Leg	muscle
42	chr15:42691200-42696200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr15:42691200-42696400	Strong transcription	Liver	Liver
44	chr15:42691200-42697000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr15:42691400-42692400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr15:42691400-42692600	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr15:42691400-42692600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr15:42691400-42692600	Strong transcription	Brain Substantia Nigra	brain
49	chr15:42691400-42692800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:42691400-42692800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links