Variant report

Variant	rs3817209
Chromosome Location	chr9:8698739-8698740
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10125358	0.83[EUR][1000 genomes]
rs10977250	0.93[CEU][hapmap];0.87[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12685924	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs1368981	0.89[EUR][1000 genomes]
rs1368982	0.89[EUR][1000 genomes]
rs1415724	0.86[CEU][hapmap]
rs1434264	0.86[CEU][hapmap];0.87[CHB][hapmap];0.89[EUR][1000 genomes]
rs1434265	0.86[CEU][hapmap];0.87[CHB][hapmap];0.89[EUR][1000 genomes]
rs1512380	0.86[CEU][hapmap]
rs1512381	0.86[CEU][hapmap]
rs16928282	0.93[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2890818	0.85[CEU][hapmap]
rs3817202	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3817208	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3817210	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4442186	0.88[CEU][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57325817	0.83[EUR][1000 genomes]
rs60000844	0.83[EUR][1000 genomes]
rs60499554	0.88[EUR][1000 genomes]
rs61002972	0.88[EUR][1000 genomes]
rs61499390	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7021243	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7030931	0.86[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7041517	0.83[EUR][1000 genomes]
rs7042493	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7042822	0.89[EUR][1000 genomes]
rs7048587	0.93[CHB][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031472	chr9:8250901-8712547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv892228	chr9:8482778-8703733	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv892232	chr9:8645448-8698875	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv892233	chr9:8645448-8702964	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv892234	chr9:8645448-8703733	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv824846	chr9:8696594-8700222	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8683000-8706000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:8693000-8699600	Enhancers	Primary hematopoietic stem cells	blood
3	chr9:8693400-8706400	Weak transcription	Fetal Brain Male	brain
4	chr9:8693800-8699800	Weak transcription	Brain Anterior Caudate	brain
5	chr9:8693800-8703400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:8693800-8706600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr9:8694400-8699400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr9:8695200-8699800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr9:8695200-8699800	Weak transcription	Brain Angular Gyrus	brain
10	chr9:8695200-8704200	Weak transcription	Brain Substantia Nigra	brain
11	chr9:8695200-8711600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr9:8695400-8700200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:8695400-8706800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr9:8696000-8703600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr9:8696200-8706600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:8696800-8706000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr9:8697000-8699400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:8697000-8704200	Weak transcription	Fetal Kidney	kidney
19	chr9:8697200-8701600	Weak transcription	Fetal Lung	lung
20	chr9:8697800-8698800	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr9:8697800-8699000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr9:8697800-8699400	Enhancers	Brain Hippocampus Middle	brain
23	chr9:8697800-8699400	Enhancers	Dnd41	blood
24	chr9:8698000-8698800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr9:8698000-8699400	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr9:8698200-8698800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr9:8698200-8698800	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr9:8698200-8698800	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr9:8698200-8698800	Enhancers	Thymus	Thymus
30	chr9:8698200-8699000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr9:8698200-8700400	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr9:8698600-8700600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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