Variant report

Variant	rs4409947
Chromosome Location	chr13:96482749-96482750
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10508027	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11616953	0.95[ASN][1000 genomes]
rs11618323	0.84[ASN][1000 genomes]
rs12430152	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12583796	1.00[YRI][hapmap]
rs1330556	0.81[ASN][1000 genomes]
rs1330557	0.81[ASN][1000 genomes]
rs17878753	0.92[ASN][1000 genomes]
rs1788062	1.00[JPT][hapmap]
rs17885081	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1854758	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3087341	0.87[ASN][1000 genomes]
rs3099362	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3099363	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3101570	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3125431	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs3125439	0.82[AMR][1000 genomes]
rs3848077	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3886352	1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3901894	1.00[YRI][hapmap]
rs4254181	0.81[ASN][1000 genomes]
rs4383020	0.88[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4491364	0.92[ASN][1000 genomes]
rs4526890	0.81[ASN][1000 genomes]
rs565297	1.00[JPT][hapmap]
rs565898	1.00[JPT][hapmap]
rs6492817	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs6492821	1.00[YRI][hapmap]
rs6492822	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72636541	0.81[ASN][1000 genomes]
rs72636556	0.81[ASN][1000 genomes]
rs72636570	0.81[ASN][1000 genomes]
rs7316996	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7318892	0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes]
rs7323408	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7331211	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7331549	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7332078	0.80[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7334320	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7334552	1.00[YRI][hapmap]
rs7335209	0.81[ASN][1000 genomes]
rs7339059	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7991405	0.88[CEU][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes]
rs7999737	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs8000018	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs816142	0.85[JPT][hapmap]
rs9302084	0.96[YRI][hapmap]
rs9516621	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9525077	0.81[ASN][1000 genomes]
rs9525079	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9561931	0.86[YRI][hapmap]
rs9561939	0.93[YRI][hapmap]
rs9584324	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9590310	0.83[AMR][1000 genomes]
rs9590316	0.84[EUR][1000 genomes]
rs9590318	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs9590321	0.84[EUR][1000 genomes]
rs9590328	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9590331	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs9590344	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	nsv832690	chr13:96330757-96508077	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	esv3509289	chr13:96461000-96505090	ZNF genes & repeats Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv3509290	chr13:96461000-96505090	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv832691	chr13:96478098-96659823	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96444400-96485600	Weak transcription	NHDF-Ad	bronchial
2	chr13:96445800-96490000	Weak transcription	HepG2	liver
3	chr13:96452000-96490600	Weak transcription	Fetal Kidney	kidney
4	chr13:96462600-96485600	Weak transcription	Hela-S3	cervix
5	chr13:96466400-96485400	Weak transcription	NHEK	skin
6	chr13:96466400-96486000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr13:96466600-96485800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr13:96466800-96485800	Weak transcription	Brain Anterior Caudate	brain
9	chr13:96467000-96485200	Weak transcription	HUVEC	blood vessel
10	chr13:96467400-96490800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr13:96468200-96489800	Weak transcription	GM12878-XiMat	blood
12	chr13:96468800-96486000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr13:96475800-96485600	Weak transcription	HMEC	breast
14	chr13:96476000-96502600	Weak transcription	Fetal Heart	heart
15	chr13:96476400-96489800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr13:96477400-96486000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr13:96478000-96485400	Weak transcription	A549	lung
18	chr13:96478000-96485600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr13:96478000-96485600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr13:96478000-96486000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr13:96478000-96486000	Weak transcription	Adipose Nuclei	Adipose
22	chr13:96478000-96498200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr13:96478000-96502600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr13:96478000-96502600	Weak transcription	Left Ventricle	heart
25	chr13:96478000-96568400	Weak transcription	Placenta	Placenta
26	chr13:96478200-96483000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr13:96478200-96485200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr13:96478200-96485400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr13:96478200-96485600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr13:96478200-96485600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr13:96478200-96485600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr13:96478200-96485600	Weak transcription	NHLF	lung
33	chr13:96478200-96485600	Weak transcription	Osteobl	bone
34	chr13:96478200-96485800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr13:96478200-96485800	Weak transcription	NH-A	brain
36	chr13:96478200-96486000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr13:96478200-96486000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr13:96478200-96486000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr13:96478200-96486400	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr13:96478200-96489200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr13:96478200-96489800	Weak transcription	Fetal Intestine Large	intestine
42	chr13:96478200-96489800	Weak transcription	Fetal Muscle Leg	muscle
43	chr13:96478200-96490000	Weak transcription	Brain Hippocampus Middle	brain
44	chr13:96478200-96490400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr13:96478200-96490400	Weak transcription	Liver	Liver
46	chr13:96478200-96490600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr13:96478200-96493600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr13:96478200-96495000	Weak transcription	Lung	lung
49	chr13:96478200-96502200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr13:96478200-96502600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links