Variant report

Variant	rs12416449
Chromosome Location	chr10:98859987-98859988
allele	C/G
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	POLR2A	chr10:98859556-98860046	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr10:98859452-98860083	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:98858093..98860956-chr10:98957219..98958927,2	K562	blood:
2	chr10:98858173..98860221-chr10:98861686..98864026,3	K562	blood:
3	chr10:98859426..98860138-chr10:98970400..98970959,2	K562	blood:

Variant related genes	Relation type
ENSG00000234855	TF binding region
ENSG00000187122	Chromatin interaction
ENSG00000234855	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10882865	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12256938	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12261620	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1336258	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1490691	0.91[JPT][hapmap]
rs1490693	0.82[ASN][1000 genomes]
rs1490694	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1490695	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2279508	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2279509	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2636796	1.00[JPT][hapmap]
rs2817691	0.91[JPT][hapmap]
rs2817693	0.91[JPT][hapmap]
rs4919071	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7074984	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7078332	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7078655	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs73322773	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7894400	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7894738	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7895198	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7895402	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7898611	0.82[ASN][1000 genomes]
rs7899087	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7911034	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[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	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	nsv1052931	chr10:98676192-98862301	Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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:24 , 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	chr10:98847400-98860600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr10:98856200-98860400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr10:98856200-98860400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr10:98856200-98860600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr10:98856400-98860400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr10:98856600-98860600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr10:98857000-98862400	Weak transcription	Right Atrium	heart
9	chr10:98857000-98862600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr10:98857000-98869200	Weak transcription	Thymus	Thymus
11	chr10:98857200-98860600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr10:98857200-98862600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr10:98857200-98869000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr10:98857400-98863200	Weak transcription	Brain Anterior Caudate	brain
15	chr10:98858200-98861200	Weak transcription	Left Ventricle	heart
16	chr10:98858600-98860800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr10:98858600-98862200	Weak transcription	Brain Germinal Matrix	brain
18	chr10:98858800-98860600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr10:98858800-98861400	Weak transcription	Right Ventricle	heart
20	chr10:98858800-98867000	Strong transcription	Fetal Thymus	thymus
21	chr10:98859000-98862200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr10:98859400-98860800	Weak transcription	Fetal Heart	heart
23	chr10:98859600-98860600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr10:98859800-98861200	Enhancers	Fetal Brain Male	brain

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