Variant report

Variant	rs17009540
Chromosome Location	chr10:49479169-49479170
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10508900	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11819269	0.87[TSI][hapmap]
rs166817	0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs17009533	0.84[EUR][1000 genomes]
rs17009537	0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs17009545	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17010208	0.82[CEU][hapmap]
rs17010407	0.82[CEU][hapmap]
rs17010430	0.82[CEU][hapmap]
rs17010447	0.82[CEU][hapmap]
rs17010454	0.82[CEU][hapmap]
rs17010455	0.82[CEU][hapmap]
rs17010496	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap]
rs17010723	0.87[TSI][hapmap]
rs17011006	1.00[AMR][1000 genomes]
rs17011019	0.82[CEU][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs17011052	0.82[CEU][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs17011060	0.82[CEU][hapmap];1.00[AMR][1000 genomes]
rs17770021	0.82[CEU][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1881733	0.87[TSI][hapmap]
rs1881734	0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs204006	0.84[EUR][1000 genomes]
rs3730160	1.00[CEU][hapmap]
rs56805036	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58555605	0.81[AMR][1000 genomes]
rs61108444	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61450644	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61840039	1.00[AMR][1000 genomes]
rs61840043	1.00[AMR][1000 genomes]
rs61840044	1.00[AMR][1000 genomes]
rs61840045	1.00[AMR][1000 genomes]
rs61840047	1.00[AMR][1000 genomes]
rs61840494	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61840495	1.00[AMR][1000 genomes]
rs61840496	1.00[AMR][1000 genomes]
rs61840497	1.00[AMR][1000 genomes]
rs61840499	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61840503	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61840508	0.81[EUR][1000 genomes]
rs61840510	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73296380	0.81[EUR][1000 genomes]
rs7915333	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895366	chr10:49299274-49576454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv895367	chr10:49333754-49491047	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv895368	chr10:49381635-49551560	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv467190	chr10:49402084-49576878	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv550811	chr10:49402084-49576878	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv895370	chr10:49421173-49484698	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49466800-49492400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:49475000-49482600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr10:49475000-49482600	Weak transcription	Right Atrium	heart
4	chr10:49475000-49482800	Weak transcription	Pancreas	Pancrea
5	chr10:49477400-49479600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr10:49478000-49482600	Weak transcription	Fetal Thymus	thymus
7	chr10:49478400-49479400	Enhancers	Brain Anterior Caudate	brain
8	chr10:49478400-49480200	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr10:49478400-49482600	Weak transcription	Dnd41	blood
10	chr10:49478800-49479800	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr10:49478800-49480000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr10:49478800-49480200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr10:49478800-49480200	Enhancers	Brain Hippocampus Middle	brain
14	chr10:49479000-49480400	Enhancers	Cortex derived primary cultured neurospheres	brain

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