Variant report

Variant	rs4885319
Chromosome Location	chr13:76159104-76159105
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	chr13:76152309..76155041-chr13:76158108..76159629,2	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11840945	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12866456	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[ASN][1000 genomes]
rs12872149	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1323694	0.84[CHB][hapmap]
rs1323696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1535726	0.96[ASN][1000 genomes]
rs1535728	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs2031235	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2274049	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2281762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2328961	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2328962	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs2876705	0.84[CHB][hapmap]
rs3812844	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3812845	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs3812846	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs4539477	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4884008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4885312	0.97[ASN][1000 genomes]
rs4885313	0.95[ASN][1000 genomes]
rs4885314	0.83[ASN][1000 genomes]
rs4885321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4885328	0.93[ASN][1000 genomes]
rs4885330	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4885331	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4885332	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4885333	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4885334	0.90[ASN][1000 genomes]
rs61960594	0.95[ASN][1000 genomes]
rs6562920	0.98[ASN][1000 genomes]
rs7139862	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7319334	0.84[CHB][hapmap]
rs7319441	0.88[ASN][1000 genomes]
rs7326807	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs7331205	0.93[ASN][1000 genomes]
rs7358977	1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs7491365	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7982534	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7982613	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7984443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7995040	0.85[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap]
rs7995889	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8000062	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8192738	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8192741	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs8192744	1.00[CEU][hapmap]
rs8192746	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8192748	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs8192750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8192751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8192753	1.00[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9318358	0.81[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap]
rs9530450	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9530453	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9530456	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9543969	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs9543994	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9543996	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9543997	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9543999	0.96[ASN][1000 genomes]
rs9544008	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9565175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9573580	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs9573584	0.97[ASN][1000 genomes]
rs9573590	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9635000	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs966058	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs966059	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs972542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975938	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761803	chr13:75943309-76161774	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv900562	chr13:76072743-76176680	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv900563	chr13:76093935-76169347	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv900565	chr13:76111280-76169347	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv900568	chr13:76123678-76159104	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv900569	chr13:76123678-76167433	Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv900570	chr13:76123678-76176680	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv900571	chr13:76123678-76207565	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers 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 target site	10 gene(s)	inside rSNPs	diseases
9	nsv900573	chr13:76130761-76159104	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv900575	chr13:76132484-76159104	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv900576	chr13:76132484-76176680	ZNF genes & repeats Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv900577	chr13:76132484-76207565	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
13	nsv900578	chr13:76136976-76167433	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	esv2751152	chr13:76144199-76288418	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4885319	COMMD6	cis	parietal	SCAN
rs4885319	UCHL3	cis	parietal	SCAN
rs4885319	COMMD6	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76124600-76183000	Weak transcription	Small Intestine	intestine
2	chr13:76124800-76164000	Weak transcription	Spleen	Spleen
3	chr13:76124800-76167600	Weak transcription	Gastric	stomach
4	chr13:76124800-76170600	Weak transcription	Colonic Mucosa	Colon
5	chr13:76125000-76192800	Weak transcription	Brain Substantia Nigra	brain
6	chr13:76125000-76209600	Weak transcription	Right Ventricle	heart
7	chr13:76125200-76173800	Weak transcription	Fetal Heart	heart
8	chr13:76125200-76177800	Weak transcription	Stomach Mucosa	stomach
9	chr13:76125400-76191000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr13:76125600-76182000	Weak transcription	Fetal Brain Male	brain
11	chr13:76129400-76180400	Weak transcription	Thymus	Thymus
12	chr13:76129600-76164000	Weak transcription	Ovary	ovary
13	chr13:76130400-76164200	Weak transcription	K562	blood
14	chr13:76135400-76164000	Weak transcription	Pancreas	Pancrea
15	chr13:76141800-76178400	Weak transcription	HepG2	liver
16	chr13:76142200-76164000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr13:76144000-76192400	Weak transcription	NHLF	lung
18	chr13:76144200-76194400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr13:76144400-76176800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr13:76148000-76165200	Weak transcription	Brain Angular Gyrus	brain
21	chr13:76148000-76173800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr13:76148000-76174200	Weak transcription	HSMMtube	muscle
23	chr13:76148000-76178600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr13:76148200-76177200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr13:76148200-76192200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr13:76148200-76203000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr13:76148200-76209600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr13:76149000-76179000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr13:76149200-76161600	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr13:76149600-76164000	Weak transcription	Brain Anterior Caudate	brain
31	chr13:76149800-76164000	Weak transcription	Adipose Nuclei	Adipose
32	chr13:76149800-76164000	Weak transcription	HMEC	breast
33	chr13:76149800-76165800	Weak transcription	Brain Germinal Matrix	brain
34	chr13:76149800-76172200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr13:76149800-76174200	Weak transcription	Psoas Muscle	Psoas
36	chr13:76149800-76180200	Weak transcription	NH-A	brain
37	chr13:76149800-76209600	Weak transcription	Lung	lung
38	chr13:76156000-76159800	ZNF genes & repeats	GM12878-XiMat	blood
39	chr13:76156400-76163200	Weak transcription	Osteobl	bone
40	chr13:76156400-76164000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr13:76156400-76164000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr13:76156800-76159200	ZNF genes & repeats	Primary T cells from cord blood	blood
43	chr13:76156800-76174000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr13:76157200-76160400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr13:76157600-76159600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr13:76157800-76159200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
47	chr13:76157800-76159200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
48	chr13:76157800-76159200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr13:76157800-76159200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr13:76157800-76159200	ZNF genes & repeats	Dnd41	blood

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