Variant report

Variant	rs12044746
Chromosome Location	chr1:62580201-62580202
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10789103	0.83[AMR][1000 genomes]
rs10789104	0.83[AMR][1000 genomes]
rs10889287	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10889292	0.81[MEX][hapmap]
rs11207904	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11207906	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11207907	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11811987	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12049510	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12071351	0.80[AMR][1000 genomes]
rs12405496	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17123111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123113	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17123114	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2012694	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013239	0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2104793	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60381716	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67557410	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs719104	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs72641122	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7418709	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528543	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9662713	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[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	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv461650	chr1:62542717-62657530	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv546417	chr1:62542717-62657530	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12044746	ECAT11	cis	multi-tissue	Pritchard
rs12044746	INADL	cis	Lymphoblastoid	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62508200-62628400	Weak transcription	Colonic Mucosa	Colon
2	chr1:62532600-62587600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:62536200-62619400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:62542400-62586800	Weak transcription	NHEK	skin
5	chr1:62542400-62587400	Weak transcription	HMEC	breast
6	chr1:62545400-62606800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:62548200-62594000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:62548400-62629800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:62550200-62607800	Weak transcription	Right Ventricle	heart
10	chr1:62551800-62594200	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:62551800-62614000	Weak transcription	Primary T cells from cord blood	blood
12	chr1:62553000-62582800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr1:62553200-62594200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:62554200-62614000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:62554400-62581600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:62555000-62589800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:62555000-62594200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:62556000-62594200	Weak transcription	Left Ventricle	heart
19	chr1:62559600-62582000	Weak transcription	Liver	Liver
20	chr1:62563600-62617400	Weak transcription	Brain Anterior Caudate	brain
21	chr1:62566000-62593600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:62566200-62582200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:62566200-62594400	Weak transcription	Aorta	Aorta
24	chr1:62566200-62603400	Weak transcription	Esophagus	oesophagus
25	chr1:62566200-62604400	Weak transcription	Lung	lung
26	chr1:62566200-62614000	Weak transcription	Adipose Nuclei	Adipose
27	chr1:62566800-62608000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:62567200-62594200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr1:62569800-62594400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:62570000-62594400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:62570200-62607800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:62575000-62587200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:62575200-62608000	Weak transcription	Fetal Kidney	kidney
34	chr1:62576600-62582600	Weak transcription	Fetal Intestine Large	intestine
35	chr1:62576600-62593800	Weak transcription	Ovary	ovary
36	chr1:62576600-62594200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:62576600-62596800	Weak transcription	Fetal Stomach	stomach
38	chr1:62576600-62618000	Weak transcription	Psoas Muscle	Psoas
39	chr1:62576800-62607800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:62578000-62584600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:62578400-62581800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:62579000-62580800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr1:62579400-62581600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:62579600-62580600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:62579800-62582000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:62580000-62589800	Weak transcription	Fetal Intestine Small	intestine
47	chr1:62580000-62594400	Weak transcription	Gastric	stomach
48	chr1:62580000-62611600	Weak transcription	Pancreas	Pancrea
49	chr1:62580200-62617200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links