Variant report

Variant	rs1648856
Chromosome Location	chr15:42233912-42233913
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42229493..42231181-chr15:42233364..42235429,2	K562	blood:
2	chr15:42232975..42235695-chr15:42236151..42238495,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11070354	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11631075	0.92[GIH][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11634233	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11638621	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12101888	0.83[CHB][hapmap];0.80[CHD][hapmap]
rs12913835	0.95[CEU][hapmap];0.89[JPT][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1426889	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1426890	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1648857	0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17687755	0.83[CHB][hapmap]
rs17687976	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17739125	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17739167	0.83[CHB][hapmap];0.80[CHD][hapmap]
rs2114477	0.92[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2665213	0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28660334	0.90[ASN][1000 genomes]
rs4924589	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924590	0.82[CHB][hapmap]
rs6493013	0.90[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6493014	0.90[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6493015	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]

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	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1038933	chr15:42138456-42309087	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
5	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv1054728	chr15:42177772-42310009	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1648856	LCMT2	cis	cerebellum	SCAN
rs1648856	SNAP23	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42221800-42236400	Weak transcription	Brain Angular Gyrus	brain
2	chr15:42222200-42249800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr15:42222800-42235200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:42222800-42237600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:42223000-42236200	Weak transcription	Colon Smooth Muscle	Colon
6	chr15:42223200-42236000	Weak transcription	HepG2	liver
7	chr15:42223200-42243800	Weak transcription	Brain Substantia Nigra	brain
8	chr15:42227200-42238400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:42227400-42243200	Weak transcription	Stomach Mucosa	stomach
10	chr15:42227600-42236200	Weak transcription	Fetal Kidney	kidney
11	chr15:42227600-42249200	Weak transcription	Small Intestine	intestine
12	chr15:42228200-42234000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr15:42228200-42234000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:42228200-42235800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:42229200-42236200	Weak transcription	Fetal Lung	lung
16	chr15:42229400-42235800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:42229600-42236000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr15:42229800-42234000	Weak transcription	Placenta	Placenta
19	chr15:42229800-42236000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr15:42230000-42234600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr15:42230000-42243200	Weak transcription	Brain Hippocampus Middle	brain
22	chr15:42230000-42248400	Strong transcription	GM12878-XiMat	blood
23	chr15:42230000-42249600	Weak transcription	K562	blood
24	chr15:42230400-42234800	Weak transcription	Primary B cells from cord blood	blood
25	chr15:42230400-42237000	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr15:42230400-42262200	Weak transcription	Thymus	Thymus
27	chr15:42230600-42235000	Genic enhancers	HMEC	breast
28	chr15:42230600-42237600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr15:42230600-42239800	Genic enhancers	HUVEC	blood vessel
30	chr15:42230600-42240000	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr15:42230800-42247000	Weak transcription	Fetal Thymus	thymus
32	chr15:42230800-42249400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:42231000-42240000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr15:42231200-42235600	Genic enhancers	HSMM	muscle
35	chr15:42231200-42235800	Genic enhancers	NHEK	skin
36	chr15:42231200-42242600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr15:42231200-42244600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr15:42231200-42249800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr15:42231400-42235400	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr15:42231400-42238800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr15:42231400-42242400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr15:42231600-42250000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr15:42231800-42239200	Strong transcription	Fetal Intestine Small	intestine
44	chr15:42232000-42235200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr15:42232000-42236200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:42232200-42234000	Genic enhancers	Primary T cells fromperipheralblood	blood
47	chr15:42232200-42234000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr15:42232200-42234600	Genic enhancers	NH-A	brain
49	chr15:42232200-42235200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr15:42232200-42235200	Strong transcription	Fetal Stomach	stomach

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