Variant report

Variant	rs1490692
Chromosome Location	chr10:98867010-98867011
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr10:98866915-98867132	H1-hESC	embryonic stem cell:	n/a	chr10:98867021-98867030

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:98865480..98867358-chr10:98868311..98871144,2	MCF-7	breast:

Variant related genes	Relation type
SLIT1	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11189008	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12256938	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1490693	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1490694	1.00[CEU][hapmap];0.89[CHB][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1490695	1.00[CEU][hapmap];0.89[CHB][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2130717	0.84[EUR][1000 genomes]
rs2279508	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2279509	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4919071	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7074984	1.00[CEU][hapmap];0.89[CHB][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7078332	1.00[CEU][hapmap];0.89[CHB][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7078655	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7081718	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7894400	1.00[CEU][hapmap];0.89[CHB][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7894738	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs7895198	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7895402	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7898611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7899087	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7911034	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[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	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv2758236	chr10:98789963-98962472	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2759777	chr10:98789963-98962472	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1037576	chr10:98791099-98873649	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1039568	chr10:98800844-98868329	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1040262	chr10:98805336-98872134	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv895913	chr10:98854410-98884402	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98841200-98869200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr10:98857000-98869200	Weak transcription	Thymus	Thymus
3	chr10:98857200-98869000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr10:98861600-98869200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr10:98863200-98869000	Weak transcription	Fetal Brain Female	brain
6	chr10:98863200-98876200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr10:98863400-98870000	Weak transcription	Brain Anterior Caudate	brain
8	chr10:98863800-98869000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:98864000-98867200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr10:98864600-98869200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr10:98866000-98867600	Enhancers	Fetal Lung	lung
12	chr10:98866600-98867800	Enhancers	Brain Germinal Matrix	brain
13	chr10:98866800-98867800	Enhancers	Fetal Intestine Large	intestine
14	chr10:98867000-98867400	Weak transcription	Fetal Thymus	thymus
15	chr10:98867000-98868000	Enhancers	Fetal Intestine Small	intestine
16	chr10:98867000-98869200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr10:98867000-98869400	Weak transcription	Right Ventricle	heart

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