Variant report

Variant	rs11139246
Chromosome Location	chr9:72157997-72157998
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10511966	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10867682	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10867766	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10867768	1.00[CEU][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11138902	0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs11139065	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11139155	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11139224	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11139228	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11139236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11139245	1.00[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]
rs11139274	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11139279	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11139289	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11139293	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11139294	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11139299	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11139300	0.81[AMR][1000 genomes]
rs1228285	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1236984	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12378157	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs12378318	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12553491	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13283450	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13286303	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13286400	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13287758	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13288354	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13289730	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13290847	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13291843	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13293185	0.84[EUR][1000 genomes]
rs13297121	0.81[JPT][hapmap]
rs13302431	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1330326	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1330331	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1331978	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1475641	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1854701	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2253778	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs2297420	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2777864	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35631039	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35693077	0.80[ASN][1000 genomes]
rs4307408	0.82[JPT][hapmap]
rs4351475	0.81[JPT][hapmap]
rs4744884	0.86[JPT][hapmap]
rs7025896	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7871891	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1035633	chr9:71995963-72176984	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1048650	chr9:72028458-72179847	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1039966	chr9:72057304-72181564	Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv466413	chr9:72100051-72160174	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv614575	chr9:72100051-72160174	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv893437	chr9:72118962-72223176	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72132200-72163000	Weak transcription	Aorta	Aorta
2	chr9:72141800-72158200	Weak transcription	Ovary	ovary
3	chr9:72143600-72158400	Weak transcription	Liver	Liver
4	chr9:72147600-72158200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:72156400-72159600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr9:72157000-72158600	Enhancers	H1 Cell Line	embryonic stem cell
7	chr9:72157000-72158600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:72157000-72158600	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr9:72157000-72158800	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr9:72157000-72158800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr9:72157000-72158800	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr9:72157000-72159000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr9:72157000-72159000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr9:72157000-72159200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:72157000-72159200	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr9:72157000-72159400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:72157200-72158200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr9:72157400-72158400	Weak transcription	Fetal Kidney	kidney
19	chr9:72157400-72158600	Enhancers	Rectal Smooth Muscle	rectum
20	chr9:72157400-72158800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr9:72157400-72158800	Enhancers	Brain Hippocampus Middle	brain
22	chr9:72157400-72158800	Enhancers	Brain Substantia Nigra	brain
23	chr9:72157400-72159000	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr9:72157600-72158400	Weak transcription	Brain Germinal Matrix	brain
25	chr9:72157600-72158600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:72157600-72158800	Enhancers	Brain Anterior Caudate	brain
27	chr9:72157600-72159200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:72157800-72158200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr9:72157800-72158200	Enhancers	Fetal Muscle Trunk	muscle
30	chr9:72157800-72158400	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr9:72157800-72158400	Enhancers	Left Ventricle	heart
32	chr9:72157800-72158400	Enhancers	Psoas Muscle	Psoas
33	chr9:72157800-72158600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr9:72157800-72158600	Enhancers	Fetal Muscle Leg	muscle
35	chr9:72157800-72158800	Enhancers	Fetal Heart	heart

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