Variant report

Variant	rs1994995
Chromosome Location	chr12:26149703-26149704
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10431215	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10459081	0.96[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10771249	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10771250	0.84[CEU][hapmap];0.89[CHB][hapmap];0.98[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap]
rs10771251	0.89[MEX][hapmap];0.90[MKK][hapmap]
rs10771253	0.81[GIH][hapmap];0.89[MEX][hapmap]
rs10771255	0.96[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10842641	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10842642	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10842645	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10842647	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10842648	0.85[CEU][hapmap];0.95[LWK][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10842651	0.88[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10842655	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10842658	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs11048363	0.88[CEU][hapmap];0.89[CHB][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11048364	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11048367	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11048370	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11048374	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12227480	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12369462	0.85[ASN][1000 genomes]
rs1513124	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs1874351	0.96[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1994997	0.83[GIH][hapmap]
rs2251618	0.94[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.85[ASN][1000 genomes]
rs2643927	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2643930	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs2643933	0.92[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729631	0.94[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap]
rs2729634	0.85[ASN][1000 genomes]
rs2729635	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs61247260	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6487522	0.92[CEU][hapmap];0.89[CHB][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7132820	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs7136804	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs7137379	0.94[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs7138742	0.94[CHB][hapmap]
rs7139241	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs7295585	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs7299421	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs7315752	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7956992	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7963754	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7964657	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7969486	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971906	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977148	0.89[MEX][hapmap]
rs7979763	0.89[CEU][hapmap];0.89[CHB][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758300	chr12:25992331-26161116	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	esv2759886	chr12:25992331-26161116	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv898931	chr12:26123345-26192936	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv522351	chr12:26127230-26149703	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1994995	BHLHE41	cis	parietal	SCAN
rs1994995	LRMP	cis	parietal	SCAN
rs1994995	FKRP	trans	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26117600-26150000	Weak transcription	Hela-S3	cervix
2	chr12:26139400-26150600	Weak transcription	Brain Angular Gyrus	brain
3	chr12:26139600-26160000	Weak transcription	Pancreas	Pancrea
4	chr12:26142200-26155600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:26143800-26151200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr12:26143800-26151200	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr12:26144000-26151200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr12:26144000-26151600	Enhancers	Colon Smooth Muscle	Colon
9	chr12:26144400-26152200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr12:26145000-26151400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr12:26145200-26151200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:26145200-26151400	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr12:26145200-26152600	Enhancers	Osteobl	bone
14	chr12:26145400-26150400	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr12:26145400-26150400	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr12:26145400-26150600	Weak transcription	Fetal Heart	heart
17	chr12:26145400-26151000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:26145600-26151800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:26145600-26163000	Weak transcription	Fetal Muscle Leg	muscle
20	chr12:26145800-26150200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:26145800-26150600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:26145800-26152400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:26145800-26153400	Weak transcription	Right Atrium	heart
24	chr12:26146000-26150200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:26146000-26150200	Weak transcription	NHEK	skin
26	chr12:26146200-26151200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:26146200-26152200	Enhancers	HSMM	muscle
28	chr12:26146200-26163000	Weak transcription	Lung	lung
29	chr12:26146600-26150200	Weak transcription	HMEC	breast
30	chr12:26146600-26150600	Weak transcription	Right Ventricle	heart
31	chr12:26146600-26155600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:26146800-26150800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:26146800-26150800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:26146800-26151000	Enhancers	HSMMtube	muscle
35	chr12:26147000-26150600	Enhancers	NHLF	lung
36	chr12:26147200-26150400	Enhancers	HUVEC	blood vessel
37	chr12:26147200-26151400	Enhancers	Rectal Smooth Muscle	rectum
38	chr12:26147400-26150600	Weak transcription	Brain Anterior Caudate	brain
39	chr12:26147800-26150200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr12:26147800-26150600	Weak transcription	Brain Hippocampus Middle	brain
41	chr12:26148000-26150400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr12:26148000-26151600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:26148000-26152200	Enhancers	Muscle Satellite Cultured Cells	--
44	chr12:26148000-26152200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:26148000-26163600	Weak transcription	Aorta	Aorta
46	chr12:26148200-26149800	Genic enhancers	NHDF-Ad	bronchial
47	chr12:26148200-26150400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr12:26148200-26150400	Enhancers	NH-A	brain
49	chr12:26148200-26150600	Weak transcription	Fetal Lung	lung
50	chr12:26148200-26150600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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