Variant report

Variant	rs11648802
Chromosome Location	chr16:71315078-71315079
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71313544..71318343-chr16:71321289..71325664,12	K562	blood:
2	chr16:71314219..71316960-chr2:160471976..160473993,2	MCF-7	breast:
3	chr16:71313476..71316261-chr16:71330808..71332669,2	MCF-7	breast:
4	chr16:71019839..71022639-chr16:71314110..71316674,2	K562	blood:

Variant related genes	Relation type
ENSG00000123636	Chromatin interaction
ENSG00000180917	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11643408	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11644378	1.00[JPT][hapmap]
rs11645087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12924136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12925681	0.91[ASN][1000 genomes]
rs146873	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171016	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17270785	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173128	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17343100	0.91[ASN][1000 genomes]
rs1834044	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs184647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1859088	1.00[ASW][hapmap];0.82[TSI][hapmap]
rs2015813	1.00[ASW][hapmap];0.82[TSI][hapmap]
rs235986	1.00[ASW][hapmap]
rs235989	1.00[ASW][hapmap];0.82[TSI][hapmap]
rs235990	1.00[ASW][hapmap];0.82[TSI][hapmap]
rs235992	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235995	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235998	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236003	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236008	1.00[ASW][hapmap];0.82[TSI][hapmap]
rs236009	1.00[ASW][hapmap];0.82[TSI][hapmap]
rs236011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236014	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236015	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs236016	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094446	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3114641	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34036373	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34364189	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34395100	0.91[ASN][1000 genomes]
rs34399179	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34538430	0.91[ASN][1000 genomes]
rs34907542	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35052014	0.91[ASN][1000 genomes]
rs35157832	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35269005	1.00[ASN][1000 genomes]
rs35794600	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35897488	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs370875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3743950	1.00[ASW][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs430445	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434108	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs446245	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs66510446	0.91[ASN][1000 genomes]
rs67275961	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71403844	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72795758	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72795760	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72795777	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758429	chr16:70807122-71316983	Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	esv2758653	chr16:70807122-71316983	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv949461	chr16:71196153-71579711	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv482374	chr16:71228600-71401617	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1062426	chr16:71307180-71423400	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11648802	BEAN	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71290200-71317200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr16:71299000-71317200	Weak transcription	Aorta	Aorta
3	chr16:71301000-71318400	Weak transcription	Pancreas	Pancrea
4	chr16:71306600-71322600	Weak transcription	Small Intestine	intestine
5	chr16:71307000-71316200	Weak transcription	HSMM	muscle
6	chr16:71307000-71317000	Weak transcription	NHEK	skin
7	chr16:71307800-71316800	Weak transcription	Left Ventricle	heart
8	chr16:71307800-71318600	Weak transcription	Psoas Muscle	Psoas
9	chr16:71308400-71317000	Weak transcription	Dnd41	blood
10	chr16:71309200-71317200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr16:71310400-71318800	Weak transcription	Thymus	Thymus
12	chr16:71310800-71317000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr16:71311000-71316800	Weak transcription	Primary B cells from cord blood	blood
14	chr16:71311000-71317000	Weak transcription	Primary T cells from cord blood	blood
15	chr16:71311000-71317600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr16:71311200-71317000	Weak transcription	GM12878-XiMat	blood
17	chr16:71311200-71317400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr16:71311400-71316200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr16:71311400-71316800	Weak transcription	K562	blood
20	chr16:71311400-71317000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr16:71312600-71315400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr16:71312600-71316200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr16:71313400-71317200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr16:71313600-71317200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr16:71314000-71316800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr16:71314000-71317000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr16:71314000-71317200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr16:71314400-71317000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr16:71314400-71317000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr16:71314600-71316800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr16:71314600-71316800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr16:71314600-71316800	Weak transcription	Brain Germinal Matrix	brain
33	chr16:71314600-71316800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr16:71314600-71317000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr16:71314600-71317200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr16:71314800-71317200	Weak transcription	Fetal Kidney	kidney
37	chr16:71315000-71316600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr16:71315000-71316800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr16:71315000-71316800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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