Variant report

Variant	rs10916646
Chromosome Location	chr1:223917907-223917908
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223915826..223918177-chr1:223937169..223939533,2	K562	blood:
2	chr1:223904247..223905976-chr1:223916920..223919197,2	MCF-7	breast:
3	chr1:223889334..223894122-chr1:223917463..223919785,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10799550	0.84[EUR][1000 genomes]
rs10916600	0.95[EUR][1000 genomes]
rs10916601	0.94[EUR][1000 genomes]
rs10916602	0.94[EUR][1000 genomes]
rs10916603	0.95[EUR][1000 genomes]
rs10916634	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[LWK][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11580460	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12066704	0.87[CEU][hapmap]
rs12069561	0.87[CEU][hapmap]
rs12070364	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12074091	0.94[EUR][1000 genomes]
rs1222138	0.87[CEU][hapmap]
rs1222141	0.87[CEU][hapmap]
rs1222145	0.84[CHB][hapmap]
rs12568612	0.87[CEU][hapmap]
rs1419305	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1539707	0.93[EUR][1000 genomes]
rs17556570	0.87[CEU][hapmap]
rs17598	0.87[CEU][hapmap]
rs1779658	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1892076	0.95[EUR][1000 genomes]
rs1892077	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2186006	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs28370014	0.93[EUR][1000 genomes]
rs28739569	0.92[EUR][1000 genomes]
rs3738373	0.87[CEU][hapmap]
rs3738374	0.87[CEU][hapmap]
rs4511081	0.83[EUR][1000 genomes]
rs4653499	0.94[EUR][1000 genomes]
rs4653500	0.95[EUR][1000 genomes]
rs4653522	0.87[CEU][hapmap]
rs61823962	0.80[EUR][1000 genomes]
rs61823965	0.83[EUR][1000 genomes]
rs61823966	0.94[EUR][1000 genomes]
rs61823967	0.94[EUR][1000 genomes]
rs61823968	0.94[EUR][1000 genomes]
rs61823980	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61823981	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6669046	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6669080	0.82[CEU][hapmap]
rs6674733	0.96[EUR][1000 genomes]
rs6702314	0.82[EUR][1000 genomes]
rs6702430	0.81[EUR][1000 genomes]
rs6703104	0.87[CEU][hapmap]
rs7412088	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7414311	0.94[EUR][1000 genomes]
rs751609	0.87[CEU][hapmap]
rs7517684	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7525446	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7543197	1.00[CEU][hapmap]
rs7547642	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7555491	1.00[CEU][hapmap];0.94[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	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv873213	chr1:223885843-223924236	Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
7	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10916646	CAPN2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223903600-223922400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:223904400-223922400	Genic enhancers	NHLF	lung
3	chr1:223906600-223921000	Weak transcription	Fetal Brain Male	brain
4	chr1:223910800-223919800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:223914400-223921800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:223914600-223918400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:223914800-223919000	Weak transcription	Brain Germinal Matrix	brain
8	chr1:223915000-223919800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:223915000-223920800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:223915000-223920800	Weak transcription	Liver	Liver
11	chr1:223915000-223921000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:223915000-223921000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:223915000-223921000	Genic enhancers	NHEK	skin
14	chr1:223915200-223918400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr1:223915200-223918400	Weak transcription	Fetal Heart	heart
16	chr1:223915200-223918400	Weak transcription	Small Intestine	intestine
17	chr1:223915200-223918600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:223915200-223919000	Weak transcription	Psoas Muscle	Psoas
19	chr1:223915200-223930800	Weak transcription	Primary T cells from cord blood	blood
20	chr1:223915400-223918000	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:223915400-223918200	Weak transcription	Stomach Mucosa	stomach
22	chr1:223915400-223918400	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:223915400-223927200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:223915400-223933000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:223915400-223933000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:223915400-223936200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr1:223915600-223918200	Weak transcription	Brain Substantia Nigra	brain
28	chr1:223915600-223918400	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:223915600-223918400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:223915600-223918400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:223915800-223918200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:223915800-223918400	Weak transcription	Brain Anterior Caudate	brain
33	chr1:223915800-223918400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr1:223915800-223918600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:223915800-223918600	Weak transcription	Ovary	ovary
36	chr1:223915800-223919000	Weak transcription	Pancreas	Pancrea
37	chr1:223915800-223931600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr1:223916000-223918600	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr1:223916200-223918400	Weak transcription	Left Ventricle	heart
40	chr1:223916200-223919000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:223916400-223918400	Weak transcription	Spleen	Spleen
42	chr1:223916400-223919000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:223916600-223918000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:223916600-223918200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:223916600-223918200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:223916600-223918200	Weak transcription	HSMMtube	muscle
47	chr1:223916600-223918400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:223916600-223918400	Weak transcription	Fetal Intestine Large	intestine
49	chr1:223916600-223918400	Weak transcription	Right Atrium	heart
50	chr1:223916600-223918400	Weak transcription	Right Ventricle	heart

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