Variant report

Variant	rs28364559
Chromosome Location	chr15:42706287-42706288
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	chr15:42698233..42703312-chr15:42703479..42708352,6	K562	blood:
2	chr15:42699538..42703312-chr15:42704209..42708483,5	K562	blood:

Variant related genes	Relation type
ENSG00000092529	Chromatin interaction

Extended variants
information (count: 197 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:191)

rs_ID	r²[population]
rs10518757	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs1062016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070363	0.82[CHB][hapmap];1.00[GIH][hapmap]
rs11070367	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11070368	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11070369	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11070371	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs1142536	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631711	1.00[EUR][1000 genomes]
rs11631756	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11631823	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11631922	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11633276	1.00[TSI][hapmap]
rs11635876	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11637010	1.00[EUR][1000 genomes]
rs11637045	1.00[EUR][1000 genomes]
rs11856797	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11856807	1.00[CHB][hapmap]
rs11858453	1.00[EUR][1000 genomes]
rs12102204	0.95[ASN][1000 genomes]
rs12437815	1.00[EUR][1000 genomes]
rs12441027	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12592200	1.00[EUR][1000 genomes]
rs12902924	1.00[CHB][hapmap]
rs12907489	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs12913755	1.00[EUR][1000 genomes]
rs12915946	0.82[CHB][hapmap]
rs12916523	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs12916792	1.00[CHB][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]
rs1659215	0.82[CHB][hapmap]
rs1659216	1.00[CHB][hapmap]
rs1659220	1.00[CHB][hapmap];0.86[GIH][hapmap]
rs1659221	1.00[CHB][hapmap]
rs1659223	1.00[CHB][hapmap];1.00[AMR][1000 genomes]
rs1659224	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs1659226	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs1678988	0.82[CHB][hapmap];1.00[GIH][hapmap]
rs1678989	0.82[CHB][hapmap]
rs1678997	1.00[EUR][1000 genomes]
rs1678998	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1678999	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs1679011	0.82[CHB][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]
rs1871156	1.00[TSI][hapmap]
rs2289293	1.00[CHB][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap]
rs2289297	1.00[CHB][hapmap]
rs2412677	1.00[EUR][1000 genomes]
rs2412681	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2412684	1.00[CHB][hapmap]
rs2412686	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2412689	1.00[CHB][hapmap]
rs2412690	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2412691	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2412694	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs2412696	1.00[EUR][1000 genomes]
rs2412697	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2412698	1.00[EUR][1000 genomes]
rs2412699	1.00[EUR][1000 genomes]
rs2412700	1.00[EUR][1000 genomes]
rs2412701	1.00[EUR][1000 genomes]
rs2412702	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2578651	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs2620374	1.00[EUR][1000 genomes]
rs2620375	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2620387	0.82[CHB][hapmap];0.87[GIH][hapmap]
rs2663096	0.82[CHB][hapmap]
rs28364400	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs28364462	0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.95[ASN][1000 genomes]
rs28364472	0.95[ASN][1000 genomes]
rs28364473	0.87[ASN][1000 genomes]
rs28364475	1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap]
rs28364491	1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[TSI][hapmap]
rs28364495	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.95[ASN][1000 genomes]
rs28364498	0.95[ASN][1000 genomes]
rs28364503	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs28364504	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.95[ASN][1000 genomes]
rs28364508	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs28364509	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs28364511	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]
rs28364519	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.98[ASN][1000 genomes]
rs28364522	0.98[ASN][1000 genomes]
rs28364523	0.93[ASN][1000 genomes]
rs28364524	0.98[ASN][1000 genomes]
rs28364526	0.98[ASN][1000 genomes]
rs28364536	1.00[EUR][1000 genomes]
rs28364544	1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[TSI][hapmap]
rs28364557	1.00[ASN][1000 genomes]
rs28602748	0.95[ASN][1000 genomes]
rs28621687	0.95[ASN][1000 genomes]
rs28726153	0.95[ASN][1000 genomes]
rs2899044	1.00[CHB][hapmap]
rs2899058	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs2918458	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs3098422	1.00[EUR][1000 genomes]
rs3101895	1.00[EUR][1000 genomes]
rs3736095	1.00[EUR][1000 genomes]
rs3736096	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs3736097	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs3743002	1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[TSI][hapmap]
rs3743003	1.00[CHB][hapmap]
rs3803342	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs4244589	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs4268723	1.00[EUR][1000 genomes]
rs4480780	1.00[EUR][1000 genomes]
rs4556762	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4583208	0.82[CHB][hapmap]
rs4595775	1.00[EUR][1000 genomes]
rs4617834	1.00[EUR][1000 genomes]
rs4923934	0.82[CHB][hapmap]
rs4923935	0.82[CHB][hapmap]
rs4923936	1.00[CHB][hapmap]
rs4923937	1.00[CHB][hapmap]
rs4923938	1.00[CHB][hapmap]
rs4923939	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4923941	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4923942	1.00[EUR][1000 genomes]
rs4924633	0.82[CHB][hapmap];1.00[GIH][hapmap]
rs4924636	0.82[CHB][hapmap];1.00[GIH][hapmap]
rs4924638	0.82[CHB][hapmap]
rs4924642	1.00[CHB][hapmap]
rs4924643	1.00[CHB][hapmap]
rs4924650	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4924651	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs4924652	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs4924655	1.00[EUR][1000 genomes]
rs4924656	1.00[EUR][1000 genomes]
rs4924657	1.00[CHB][hapmap]
rs4924659	1.00[EUR][1000 genomes]
rs4924662	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs4924663	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs4924664	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs4924665	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs4924666	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs4924667	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs4924668	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4924669	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4924670	1.00[CHB][hapmap]
rs4924671	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs5028174	1.00[EUR][1000 genomes]
rs5029919	1.00[CHB][hapmap]
rs57052341	1.00[EUR][1000 genomes]
rs607959	0.82[CHB][hapmap]
rs613090	0.82[CHB][hapmap];1.00[GIH][hapmap]
rs62022303	0.95[ASN][1000 genomes]
rs62022305	0.95[ASN][1000 genomes]
rs638240	0.82[CHB][hapmap];1.00[GIH][hapmap]
rs6493026	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6493028	1.00[EUR][1000 genomes]
rs6493029	1.00[EUR][1000 genomes]
rs6493034	1.00[CHB][hapmap]
rs6493037	1.00[EUR][1000 genomes]
rs6493041	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6493046	0.95[ASN][1000 genomes]
rs7161982	1.00[CHB][hapmap]
rs7163941	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs7164196	1.00[TSI][hapmap]
rs7167306	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs7168121	0.91[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs7169279	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs7169553	1.00[CHB][hapmap]
rs7170592	1.00[EUR][1000 genomes]
rs7170943	1.00[CHB][hapmap]
rs7171379	1.00[EUR][1000 genomes]
rs7171709	1.00[EUR][1000 genomes]
rs7173358	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs7176724	1.00[EUR][1000 genomes]
rs7177193	1.00[CHB][hapmap]
rs7178396	1.00[ASN][1000 genomes]
rs7183843	1.00[CHB][hapmap]
rs8023568	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs8023678	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs8023714	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs8024390	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs8025364	1.00[CHB][hapmap]
rs8030650	0.82[CHB][hapmap]
rs8031541	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8031735	0.82[CHB][hapmap];0.87[GIH][hapmap]
rs8037100	0.82[CHB][hapmap]
rs8037627	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs8040698	1.00[EUR][1000 genomes]
rs8042603	0.95[ASN][1000 genomes]
rs8043515	1.00[CHB][hapmap]
rs9920851	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28364559	SAMD12	trans	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42678600-42706800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:42679000-42706800	Weak transcription	Right Atrium	heart
3	chr15:42689000-42712400	Weak transcription	Fetal Brain Male	brain
4	chr15:42689800-42706600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr15:42692600-42708400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:42694600-42750600	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr15:42694800-42706800	Weak transcription	GM12878-XiMat	blood
8	chr15:42694800-42708400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:42695000-42716000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr15:42697000-42706400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr15:42697000-42708400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:42697200-42707800	Weak transcription	K562	blood
13	chr15:42698400-42707000	Weak transcription	Hela-S3	cervix
14	chr15:42698400-42708400	Weak transcription	Fetal Kidney	kidney
15	chr15:42698600-42738400	Strong transcription	Fetal Muscle Leg	muscle
16	chr15:42699200-42741600	Strong transcription	Fetal Muscle Trunk	muscle
17	chr15:42700000-42732400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:42700200-42713600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr15:42700600-42710200	Strong transcription	Brain Anterior Caudate	brain
20	chr15:42700800-42708200	Weak transcription	Stomach Mucosa	stomach
21	chr15:42700800-42732000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:42700800-42747200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr15:42701000-42719200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:42701000-42738800	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr15:42701200-42766600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr15:42701400-42710200	Strong transcription	Brain Cingulate Gyrus	brain
27	chr15:42701400-42710200	Strong transcription	Brain Hippocampus Middle	brain
28	chr15:42701400-42710200	Strong transcription	Brain Substantia Nigra	brain
29	chr15:42701400-42732600	Strong transcription	Adipose Nuclei	Adipose
30	chr15:42701600-42744200	Strong transcription	Stomach Smooth Muscle	stomach
31	chr15:42701800-42732400	Strong transcription	Fetal Intestine Large	intestine
32	chr15:42702000-42706400	Weak transcription	HepG2	liver
33	chr15:42702000-42711400	Strong transcription	Primary T cells from cord blood	blood
34	chr15:42702200-42719200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:42702200-42750200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr15:42702400-42710200	Strong transcription	Primary B cells from cord blood	blood
37	chr15:42702400-42732600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr15:42702400-42744200	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr15:42702400-42744200	Strong transcription	Liver	Liver
40	chr15:42702600-42707400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr15:42702600-42708200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr15:42702600-42708400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr15:42702600-42709800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr15:42702600-42713000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr15:42702600-42719400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr15:42702600-42724000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:42702600-42732400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:42702600-42738800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:42702600-42744400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr15:42702800-42706600	Strong transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links