Variant report

Variant	rs2407707
Chromosome Location	chr15:42659350-42659351
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	chr15:42657935..42659641-chr15:42660404..42662394,2	K562	blood:

Extended variants
information (count: 138 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1062038	0.81[CEU][hapmap]
rs10775126	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10851407	0.80[EUR][1000 genomes]
rs10851408	0.80[EUR][1000 genomes]
rs10851409	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11070370	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11631917	0.80[EUR][1000 genomes]
rs11631983	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11638784	0.91[EUR][1000 genomes]
rs12437600	0.82[ASN][1000 genomes]
rs12438369	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12438453	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12438509	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[ASN][1000 genomes]
rs12438562	0.88[EUR][1000 genomes]
rs12440087	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12441016	0.84[ASN][1000 genomes]
rs12441642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12441700	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12594162	0.80[EUR][1000 genomes]
rs12917101	0.80[EUR][1000 genomes]
rs1359003	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1359004	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1659212	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1659217	0.88[EUR][1000 genomes]
rs1678985	1.00[CEU][hapmap]
rs1678986	1.00[CEU][hapmap]
rs1679009	1.00[CEU][hapmap]
rs1679010	1.00[CEU][hapmap]
rs16972887	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs16973008	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[ASN][1000 genomes]
rs16973045	0.86[CHB][hapmap];0.92[ASN][1000 genomes]
rs16973060	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1703750	1.00[CEU][hapmap]
rs1703755	0.91[CEU][hapmap]
rs1712418	1.00[CEU][hapmap]
rs2138831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2289295	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2412682	0.80[EUR][1000 genomes]
rs2412685	0.80[EUR][1000 genomes]
rs2412688	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2412705	0.88[EUR][1000 genomes]
rs2412709	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28364388	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28364390	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28364393	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs28364416	0.87[EUR][1000 genomes]
rs2918459	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2918461	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs3743005	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3743006	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs3743007	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3743008	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3825785	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3850774	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4329897	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4506867	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4923932	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4923940	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4923943	0.85[EUR][1000 genomes]
rs4923945	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4924627	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4924630	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4924644	0.89[ASN][1000 genomes]
rs4924645	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs4924648	0.80[EUR][1000 genomes]
rs4924653	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4924658	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4924660	0.85[EUR][1000 genomes]
rs4924672	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4924673	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4924674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4924675	1.00[JPT][hapmap]
rs55882551	0.89[ASN][1000 genomes]
rs56257215	0.89[ASN][1000 genomes]
rs56670003	0.89[ASN][1000 genomes]
rs56702977	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56987883	0.95[ASN][1000 genomes]
rs57002846	0.83[EUR][1000 genomes]
rs57134130	0.95[ASN][1000 genomes]
rs57347762	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57933952	0.89[ASN][1000 genomes]
rs57973092	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs57976413	0.89[ASN][1000 genomes]
rs58292736	0.89[ASN][1000 genomes]
rs58313689	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58712370	0.95[ASN][1000 genomes]
rs59094161	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs59132828	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59138723	0.89[ASN][1000 genomes]
rs59320762	0.95[ASN][1000 genomes]
rs59974698	0.89[ASN][1000 genomes]
rs60634548	0.89[ASN][1000 genomes]
rs61069354	0.89[ASN][1000 genomes]
rs61133768	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs622442	1.00[CEU][hapmap]
rs633934	1.00[CEU][hapmap]
rs6493027	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6493033	0.89[ASN][1000 genomes]
rs6493045	0.85[EUR][1000 genomes]
rs660126	1.00[CEU][hapmap]
rs677878	1.00[CEU][hapmap]
rs7163986	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs7166785	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7168709	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7175863	0.88[EUR][1000 genomes]
rs7177120	0.82[EUR][1000 genomes]
rs7179203	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7180279	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7181742	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7183015	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7183546	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs73398938	0.89[ASN][1000 genomes]
rs73400993	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73402707	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73403365	0.89[ASN][1000 genomes]
rs73407488	0.89[ASN][1000 genomes]
rs73409577	0.87[ASN][1000 genomes]
rs751572	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs765830	0.83[EUR][1000 genomes]
rs8024113	0.80[EUR][1000 genomes]
rs8024732	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs8025601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8026198	0.84[EUR][1000 genomes]
rs8027016	0.89[ASN][1000 genomes]
rs8031315	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs8036187	1.00[CEU][hapmap]
rs8036380	0.88[EUR][1000 genomes]
rs8036596	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs8037020	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs8041951	0.95[ASN][1000 genomes]
rs9920921	1.00[CEU][hapmap];0.88[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	nsv904133	chr15:42528982-42681057	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42645600-42663000	Weak transcription	NHDF-Ad	bronchial
2	chr15:42645600-42663600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr15:42645600-42677800	Weak transcription	Spleen	Spleen
4	chr15:42646000-42662600	Weak transcription	Brain Substantia Nigra	brain
5	chr15:42646000-42678600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:42647800-42678200	Weak transcription	Ovary	ovary
7	chr15:42649800-42659800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:42649800-42673200	Weak transcription	Thymus	Thymus
9	chr15:42650200-42659600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr15:42650600-42661000	Weak transcription	Esophagus	oesophagus
11	chr15:42650600-42661600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr15:42650800-42659400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:42650800-42664000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:42651200-42659600	Weak transcription	Primary T cells from cord blood	blood
15	chr15:42652400-42660600	Weak transcription	Aorta	Aorta
16	chr15:42652400-42665400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:42652800-42684400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr15:42653200-42691600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr15:42653400-42659600	Weak transcription	Fetal Intestine Small	intestine
20	chr15:42654200-42677800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr15:42654400-42665400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:42654800-42669400	Weak transcription	Liver	Liver
23	chr15:42656000-42678800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:42656800-42663600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr15:42656800-42693400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:42656800-42697800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr15:42657000-42665600	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:42657000-42665600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr15:42657200-42659400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr15:42657200-42660200	Weak transcription	Fetal Muscle Leg	muscle
31	chr15:42657200-42665800	Weak transcription	Left Ventricle	heart
32	chr15:42657200-42678800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr15:42657800-42659400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr15:42657800-42660200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr15:42658400-42660800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:42658600-42659400	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr15:42659000-42659400	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr15:42659200-42659400	Weak transcription	Primary B cells from cord blood	blood
39	chr15:42659200-42659600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:42659200-42659600	Enhancers	Lung	lung
41	chr15:42659200-42659600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr15:42659200-42660200	Weak transcription	Psoas Muscle	Psoas

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