Variant report

Variant	rs11990096
Chromosome Location	chr8:9195378-9195379
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:9007894..9008784-chr8:9195169..9196375,4	MCF-7	breast:
2	chr8:9177871..9178799-chr8:9195168..9196018,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173281	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10099512	1.00[CHB][hapmap]
rs10106829	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11778774	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11779870	1.00[CHB][hapmap]
rs11781511	0.86[ASN][1000 genomes]
rs12543276	0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs13255273	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13264007	0.86[ASN][1000 genomes]
rs13265179	0.86[ASN][1000 genomes]
rs13274716	0.86[ASN][1000 genomes]
rs13279173	1.00[CHB][hapmap]
rs1461729	0.86[ASN][1000 genomes]
rs17660635	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17661330	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs17716118	1.00[CHB][hapmap]
rs2054345	0.86[ASN][1000 genomes]
rs2126259	0.86[ASN][1000 genomes]
rs2126260	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2126261	1.00[CHB][hapmap]
rs2126263	0.86[ASN][1000 genomes]
rs2126264	0.86[ASN][1000 genomes]
rs2169385	0.86[ASN][1000 genomes]
rs2169387	0.86[ASN][1000 genomes]
rs28494016	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28529330	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs330090	0.87[ASN][1000 genomes]
rs330091	1.00[ASN][1000 genomes]
rs330092	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs330093	0.87[ASN][1000 genomes]
rs330095	0.87[ASN][1000 genomes]
rs330096	0.87[ASN][1000 genomes]
rs34025891	0.86[ASN][1000 genomes]
rs34271262	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34906420	0.86[ASN][1000 genomes]
rs35584813	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35899262	0.86[ASN][1000 genomes]
rs35922567	0.80[AMR][1000 genomes]
rs36090863	0.81[AMR][1000 genomes]
rs4240624	0.86[ASN][1000 genomes]
rs4332138	0.86[ASN][1000 genomes]
rs4841132	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs4841133	0.86[ASN][1000 genomes]
rs60191553	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6601299	0.86[ASN][1000 genomes]
rs6984305	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs6985493	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6998846	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7002551	1.00[CHB][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs7004769	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73535309	0.86[ASN][1000 genomes]
rs7357361	1.00[CHB][hapmap]
rs7464067	0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs9650620	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9772631	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs983308	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs983309	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs983310	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs983311	1.00[ASN][1000 genomes]
rs9987289	1.00[CHB][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv949434	chr8:8993551-9318404	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1018847	chr8:9017110-9216354	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1022967	chr8:9023771-9261351	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv539462	chr8:9023771-9261351	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv530864	chr8:9097498-9914548	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv497927	chr8:9097611-9544519	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv1030524	chr8:9183482-9412833	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv6073	chr8:9189800-9234741	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv890341	chr8:9192927-9243428	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9187000-9195400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr8:9189400-9199800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr8:9190800-9195400	Weak transcription	Fetal Intestine Large	intestine
4	chr8:9192200-9196200	Enhancers	Brain Hippocampus Middle	brain
5	chr8:9192400-9195400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr8:9193000-9196400	Enhancers	Fetal Heart	heart
7	chr8:9193600-9196000	Enhancers	Left Ventricle	heart
8	chr8:9193600-9197000	Enhancers	Liver	Liver
9	chr8:9193800-9195400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr8:9193800-9195600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr8:9193800-9195600	Weak transcription	Brain Angular Gyrus	brain
12	chr8:9193800-9195600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr8:9194200-9195400	Weak transcription	Brain Anterior Caudate	brain
14	chr8:9194200-9195400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr8:9194400-9195400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr8:9194400-9195400	Weak transcription	Brain Substantia Nigra	brain
17	chr8:9194400-9196200	Enhancers	Fetal Stomach	stomach
18	chr8:9194600-9196000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr8:9194600-9196000	Enhancers	Right Ventricle	heart
20	chr8:9194800-9195800	Weak transcription	Placenta	Placenta
21	chr8:9194800-9195800	Enhancers	Right Atrium	heart
22	chr8:9194800-9196200	Enhancers	Fetal Muscle Leg	muscle
23	chr8:9194800-9196200	Enhancers	Ovary	ovary
24	chr8:9195000-9196000	Enhancers	Fetal Lung	lung
25	chr8:9195200-9195800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr8:9195200-9195800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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