Variant report

Variant	rs11641053
Chromosome Location	chr16:81365974-81365975
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	chr16:81298425..81302121-chr16:81361527..81366002,4	MCF-7	breast:
2	chr16:81358702..81362075-chr16:81365943..81367712,3	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1035572	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11639818	0.93[GIH][hapmap];0.80[TSI][hapmap]
rs11641563	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11641879	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11641889	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11648005	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11648201	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12597273	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12920172	0.81[GIH][hapmap]
rs16955064	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1946286	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2216768	0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4888139	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4888140	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4889306	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4889309	0.80[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs60369762	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6564872	0.81[CHD][hapmap]
rs7196981	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7197360	0.81[EUR][1000 genomes]
rs7200073	0.90[CEU][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8062704	0.81[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.80[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9934557	0.81[GIH][hapmap]

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	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv1058519	chr16:81177767-81735333	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv948448	chr16:81198147-81906766	Enhancers Flanking Active TSS Weak transcription Strong transcription 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	37 gene(s)	inside rSNPs	diseases
5	nsv1061359	chr16:81349826-81471867	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
6	nsv542992	chr16:81349826-81471867	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
7	nsv524464	chr16:81359467-81365974	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11641053	GAN	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81350000-81371200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr16:81350000-81372000	Weak transcription	Primary B cells from cord blood	blood
3	chr16:81350000-81373200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr16:81350000-81375000	Weak transcription	Fetal Intestine Large	intestine
5	chr16:81350400-81367600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr16:81350400-81370400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr16:81350400-81373200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr16:81350600-81367600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr16:81350600-81372800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr16:81351200-81369800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr16:81351400-81368800	Weak transcription	Dnd41	blood
12	chr16:81351400-81371200	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr16:81352800-81366000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr16:81352800-81367400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr16:81353200-81367800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr16:81353400-81373200	Weak transcription	HUVEC	blood vessel
17	chr16:81353400-81390400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr16:81353600-81366200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr16:81353800-81372600	Weak transcription	A549	lung
20	chr16:81354000-81371400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr16:81354200-81391600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr16:81354400-81372800	Weak transcription	HSMM	muscle
23	chr16:81355600-81371600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr16:81357800-81375800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr16:81358600-81367400	Weak transcription	Right Ventricle	heart
26	chr16:81358800-81367400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr16:81358800-81369600	Weak transcription	K562	blood
28	chr16:81358800-81372200	Weak transcription	Right Atrium	heart
29	chr16:81358800-81372400	Weak transcription	Lung	lung
30	chr16:81359000-81369400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr16:81359000-81370000	Weak transcription	HepG2	liver
32	chr16:81359200-81366000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr16:81359200-81369000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr16:81359200-81370400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr16:81359800-81370400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr16:81360400-81367600	Weak transcription	Primary T cells from cord blood	blood
37	chr16:81360600-81371200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr16:81360600-81373000	Weak transcription	Brain Angular Gyrus	brain
39	chr16:81360800-81372000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr16:81361400-81370200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr16:81363000-81366000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr16:81363000-81372600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr16:81363200-81366800	Weak transcription	Brain Germinal Matrix	brain
44	chr16:81363600-81366000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr16:81363600-81367200	Weak transcription	Fetal Lung	lung
46	chr16:81363600-81368200	Weak transcription	Gastric	stomach
47	chr16:81363800-81366000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr16:81363800-81369600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr16:81363800-81379400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr16:81364000-81367800	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links