Variant report

Variant	rs3803342
Chromosome Location	chr15:42689238-42689239
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	chr15:42686331..42689560-chr15:42693488..42696057,3	K562	blood:
2	chr15:42353338..42356078-chr15:42687928..42689518,2	K562	blood:

Variant related genes	Relation type
ENSG00000092529	Chromatin interaction

Extended variants
information (count: 188 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:181)

rs_ID	r²[population]
rs10518757	1.00[CHB][hapmap]
rs1062016	0.95[ASN][1000 genomes]
rs11070367	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11070368	1.00[CHB][hapmap]
rs11070369	1.00[CHB][hapmap]
rs11070371	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs1142536	0.95[ASN][1000 genomes]
rs11631756	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11631823	1.00[CHB][hapmap]
rs11631922	1.00[CHB][hapmap]
rs11633276	1.00[EUR][1000 genomes]
rs11635876	1.00[CHB][hapmap]
rs11856797	1.00[CHB][hapmap]
rs11856807	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs12102204	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441027	1.00[CHB][hapmap]
rs12593511	1.00[EUR][1000 genomes]
rs12902924	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs12907489	1.00[CHB][hapmap]
rs12911561	1.00[EUR][1000 genomes]
rs12916523	1.00[CHB][hapmap]
rs12916792	1.00[CHB][hapmap]
rs1659214	1.00[EUR][1000 genomes]
rs1659216	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs1659220	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs1659221	1.00[CHB][hapmap]
rs1659223	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs1659224	1.00[CHB][hapmap]
rs1659225	1.00[EUR][1000 genomes]
rs1659226	1.00[CHB][hapmap]
rs1678998	1.00[CHB][hapmap]
rs1678999	1.00[CHB][hapmap]
rs1712442	0.83[YRI][hapmap]
rs1871156	1.00[EUR][1000 genomes]
rs2244773	1.00[EUR][1000 genomes]
rs2289293	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2289297	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2412675	1.00[EUR][1000 genomes]
rs2412676	1.00[EUR][1000 genomes]
rs2412678	1.00[EUR][1000 genomes]
rs2412681	1.00[CHB][hapmap]
rs2412683	1.00[EUR][1000 genomes]
rs2412684	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2412686	1.00[CHB][hapmap]
rs2412689	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2412690	1.00[CHB][hapmap]
rs2412691	1.00[CHB][hapmap]
rs2412694	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2412695	1.00[EUR][1000 genomes]
rs2412697	1.00[CHB][hapmap]
rs2412702	1.00[CHB][hapmap]
rs2412716	1.00[EUR][1000 genomes]
rs2578651	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2595935	1.00[EUR][1000 genomes]
rs2620372	1.00[EUR][1000 genomes]
rs2620375	1.00[CHB][hapmap]
rs2663096	0.84[YRI][hapmap]
rs28364379	1.00[EUR][1000 genomes]
rs28364398	1.00[EUR][1000 genomes]
rs28364400	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs28364462	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28364475	1.00[CHB][hapmap]
rs28364491	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs28364495	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364498	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364500	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28364503	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs28364504	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28364507	1.00[EUR][1000 genomes]
rs28364508	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs28364509	1.00[CHB][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28364511	1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28364519	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28364522	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28364523	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28364524	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28364526	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28364540	1.00[EUR][1000 genomes]
rs28364541	1.00[EUR][1000 genomes]
rs28364544	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs28364557	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28364559	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs28489155	1.00[EUR][1000 genomes]
rs28602748	0.91[ASN][1000 genomes]
rs28621687	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28726153	0.91[ASN][1000 genomes]
rs28745879	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2899044	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2899058	1.00[EUR][1000 genomes]
rs2918458	1.00[CHB][hapmap]
rs3736096	1.00[CHB][hapmap]
rs3736097	1.00[CHB][hapmap]
rs3743002	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs3743003	1.00[CHB][hapmap]
rs4244589	1.00[CHB][hapmap]
rs4556762	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs4923936	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs4923937	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs4923938	1.00[CHB][hapmap]
rs4923939	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs4923941	1.00[CHB][hapmap]
rs4924640	1.00[EUR][1000 genomes]
rs4924641	1.00[EUR][1000 genomes]
rs4924642	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs4924643	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs4924649	1.00[EUR][1000 genomes]
rs4924650	1.00[CHB][hapmap]
rs4924651	1.00[CHB][hapmap]
rs4924652	1.00[CHB][hapmap]
rs4924657	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs4924662	1.00[CHB][hapmap]
rs4924663	1.00[CHB][hapmap]
rs4924664	1.00[CHB][hapmap]
rs4924665	1.00[CHB][hapmap]
rs4924666	1.00[CHB][hapmap]
rs4924667	1.00[CHB][hapmap]
rs4924668	1.00[CHB][hapmap]
rs4924669	1.00[CHB][hapmap]
rs4924670	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs4924671	1.00[CHB][hapmap]
rs5028173	1.00[EUR][1000 genomes]
rs5029919	1.00[CHB][hapmap]
rs602270	0.84[YRI][hapmap]
rs603468	0.84[YRI][hapmap]
rs607959	0.84[YRI][hapmap]
rs62022303	0.91[ASN][1000 genomes]
rs62022305	0.91[ASN][1000 genomes]
rs638240	0.83[YRI][hapmap]
rs6493024	1.00[EUR][1000 genomes]
rs6493026	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs6493031	1.00[EUR][1000 genomes]
rs6493034	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs6493038	1.00[EUR][1000 genomes]
rs6493041	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs6493046	1.00[ASN][1000 genomes]
rs6493047	1.00[EUR][1000 genomes]
rs6493051	1.00[EUR][1000 genomes]
rs652192	0.84[YRI][hapmap]
rs655704	1.00[EUR][1000 genomes]
rs659354	0.84[YRI][hapmap]
rs67384392	1.00[EUR][1000 genomes]
rs683227	0.84[YRI][hapmap]
rs683579	0.84[YRI][hapmap]
rs7161982	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs7163941	1.00[CHB][hapmap]
rs7164196	1.00[EUR][1000 genomes]
rs7164484	1.00[EUR][1000 genomes]
rs7167306	1.00[CHB][hapmap]
rs7168121	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7169279	1.00[CHB][hapmap]
rs7169553	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs7169941	0.83[AMR][1000 genomes]
rs7170943	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs7173358	1.00[CHB][hapmap]
rs7177193	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs7177463	1.00[EUR][1000 genomes]
rs7177521	1.00[EUR][1000 genomes]
rs7178396	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7181940	1.00[EUR][1000 genomes]
rs7182777	1.00[EUR][1000 genomes]
rs7183399	1.00[EUR][1000 genomes]
rs7183843	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs8023568	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs8023678	1.00[CHB][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs8023714	1.00[CHB][hapmap]
rs8024390	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs8025364	1.00[CHB][hapmap]
rs8031541	0.95[ASN][1000 genomes]
rs8036149	1.00[EUR][1000 genomes]
rs8036163	1.00[EUR][1000 genomes]
rs8037100	0.82[JPT][hapmap]
rs8037627	1.00[CHB][hapmap]
rs8040720	1.00[EUR][1000 genomes]
rs8042603	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043033	1.00[EUR][1000 genomes]
rs8043515	1.00[CHB][hapmap]
rs8108	0.83[YRI][hapmap]
rs936603	1.00[EUR][1000 genomes]
rs9920851	1.00[CHB][hapmap];1.00[EUR][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:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42653200-42691600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:42656800-42693400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:42656800-42697800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:42663000-42691400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:42673400-42691800	Weak transcription	Primary T cells from cord blood	blood
6	chr15:42674000-42694400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:42675200-42702800	Weak transcription	Colon Smooth Muscle	Colon
8	chr15:42675600-42691600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr15:42676800-42693200	Weak transcription	Fetal Stomach	stomach
10	chr15:42677000-42693400	Weak transcription	GM12878-XiMat	blood
11	chr15:42678600-42691200	Weak transcription	Gastric	stomach
12	chr15:42678600-42706800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:42678800-42691600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr15:42678800-42694000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr15:42678800-42702800	Weak transcription	NHLF	lung
16	chr15:42679000-42691400	Weak transcription	Thymus	Thymus
17	chr15:42679000-42706800	Weak transcription	Right Atrium	heart
18	chr15:42679200-42691600	Weak transcription	Brain Anterior Caudate	brain
19	chr15:42679200-42694000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr15:42679600-42691400	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr15:42680000-42693200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:42680200-42690200	Strong transcription	Fetal Muscle Leg	muscle
23	chr15:42680200-42691400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:42680200-42694000	Weak transcription	Left Ventricle	heart
25	chr15:42680200-42696400	Weak transcription	HSMMtube	muscle
26	chr15:42680600-42691200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:42680600-42693600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr15:42681600-42695400	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr15:42681800-42694600	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr15:42682000-42691600	Weak transcription	Adipose Nuclei	Adipose
31	chr15:42682000-42691800	Weak transcription	Ovary	ovary
32	chr15:42682400-42691600	Weak transcription	Aorta	Aorta
33	chr15:42682600-42691400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr15:42683800-42704600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr15:42684000-42691400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr15:42685000-42693800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr15:42685200-42693600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr15:42685800-42691400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr15:42686200-42694200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr15:42686400-42691400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr15:42686800-42689600	Enhancers	Fetal Intestine Large	intestine
42	chr15:42687400-42689400	Strong transcription	Spleen	Spleen
43	chr15:42687400-42689600	Strong transcription	Fetal Muscle Trunk	muscle
44	chr15:42687400-42691600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr15:42687800-42691400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:42687800-42691800	Weak transcription	Pancreas	Pancrea
47	chr15:42688000-42691400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr15:42688200-42693800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:42688400-42691400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr15:42688400-42691400	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links