Variant report

Variant	rs10124554
Chromosome Location	chr9:16512777-16512778
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10117527	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10118463	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10118467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10119249	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10122434	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123674	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10124550	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10756756	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs10962461	0.85[JPT][hapmap]
rs10962468	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10962470	0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12377857	0.97[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1927631	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs28555116	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7021958	0.90[CHB][hapmap]
rs7024707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7028447	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7028503	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7028666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7033269	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7035706	0.83[ASN][1000 genomes]
rs7043485	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7044580	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73417442	0.94[EUR][1000 genomes]
rs7848343	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7848584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7848696	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7849139	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7863830	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv892646	chr9:16476144-16514375	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS	lncRNA	n/a	inside rSNPs	diseases
6	nsv892647	chr9:16476144-16521534	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv466265	chr9:16484731-16516941	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	n/a	n/a	inside rSNPs	diseases
8	nsv613670	chr9:16484731-16516941	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16483200-16513600	Weak transcription	Psoas Muscle	Psoas
2	chr9:16500400-16514000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:16505400-16514000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr9:16506000-16513600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr9:16506000-16514200	Weak transcription	NHDF-Ad	bronchial
6	chr9:16506000-16515200	Weak transcription	Adipose Nuclei	Adipose
7	chr9:16506200-16515000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr9:16506600-16514000	Weak transcription	Fetal Lung	lung
9	chr9:16510200-16514800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr9:16510200-16515000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr9:16510200-16515200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:16510200-16515400	Weak transcription	Aorta	Aorta
13	chr9:16510400-16513600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:16510400-16513800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr9:16510400-16513800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:16510400-16513800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:16510400-16513800	Weak transcription	Fetal Stomach	stomach
18	chr9:16510400-16514000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:16510400-16514000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:16510400-16514000	Weak transcription	HSMMtube	muscle
21	chr9:16510400-16514200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr9:16510400-16515000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:16510400-16515200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:16510600-16514000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr9:16510600-16514000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:16510600-16514000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr9:16510600-16514000	Weak transcription	HSMM	muscle
28	chr9:16510600-16514800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr9:16510600-16514800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr9:16510600-16514800	Weak transcription	NH-A	brain
31	chr9:16510600-16515000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr9:16510800-16513600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr9:16510800-16513800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr9:16510800-16514000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr9:16510800-16514000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr9:16510800-16514000	Weak transcription	Osteobl	bone
37	chr9:16510800-16514200	Weak transcription	A549	lung
38	chr9:16511000-16512800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr9:16511000-16513600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr9:16511000-16513800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr9:16511000-16514000	Weak transcription	Colon Smooth Muscle	Colon
42	chr9:16511000-16515000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr9:16511200-16513800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr9:16511200-16514000	Weak transcription	NHLF	lung
45	chr9:16511400-16513600	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr9:16511400-16514800	Weak transcription	HUVEC	blood vessel
47	chr9:16512000-16515400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr9:16512400-16517400	Enhancers	Ovary	ovary
49	chr9:16512600-16514000	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links