Variant report

Variant	rs11928990
Chromosome Location	chr3:134568974-134568975
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	chr3:134568888-134569416	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr3:134568868-134569369	H1-neurons	neurons:	n/a	n/a
3	REST	chr3:134568498-134569587	H1-neurons	neurons:	n/a	chr3:134568530-134568548 chr3:134568529-134568549

Variant related genes	Relation type
EPHB1	TF binding region

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12496060	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13073658	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13079457	0.89[CHB][hapmap]
rs13090529	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13090749	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13090758	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13091440	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1949305	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2292659	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2292660	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2895697	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34894066	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35520698	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35600864	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35988574	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732569	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6439529	0.89[CHB][hapmap]
rs6762261	0.89[CHB][hapmap]
rs6782516	0.89[CHB][hapmap]
rs6797336	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6801877	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72984008	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7634094	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877515	chr3:134460368-134591138	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1009634	chr3:134543259-134820208	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv536720	chr3:134543259-134820208	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1000277	chr3:134546080-134970837	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134549800-134569400	Weak transcription	Fetal Brain Male	brain
2	chr3:134565600-134569600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:134566000-134569600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:134566200-134569200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:134566200-134569400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:134566600-134569000	Weak transcription	Adipose Nuclei	Adipose
7	chr3:134566600-134569200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:134566600-134569200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:134566800-134569400	Weak transcription	Left Ventricle	heart
10	chr3:134566800-134569800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr3:134567200-134569600	Weak transcription	HUVEC	blood vessel
12	chr3:134567200-134576000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:134567800-134571600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr3:134568200-134570800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:134568200-134571400	Enhancers	GM12878-XiMat	blood
16	chr3:134568400-134570800	Enhancers	Spleen	Spleen
17	chr3:134568400-134572200	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr3:134568600-134569000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:134568600-134570000	Enhancers	Psoas Muscle	Psoas
20	chr3:134568600-134571400	Enhancers	Fetal Muscle Leg	muscle
21	chr3:134568800-134569600	Enhancers	Dnd41	blood

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