Variant report

Variant	rs3780307
Chromosome Location	chr9:27206274-27206275
allele	A/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	CEBPB	chr9:27206129-27206382	HepG2	liver:	n/a	chr9:27206247-27206258 chr9:27206247-27206260

Variant related genes	Relation type
ENSG00000232867	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10115251	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10118142	0.89[ASN][1000 genomes]
rs10967765	0.82[ASN][1000 genomes]
rs10967767	0.86[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11791837	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12236499	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1334810	0.83[YRI][hapmap]
rs1413827	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1413828	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1413829	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1413832	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2282230	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3780314	0.94[CHB][hapmap];0.93[YRI][hapmap]
rs3780315	0.83[CEU][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs538294	0.83[YRI][hapmap]
rs641848	0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[ASN][1000 genomes]
rs654494	0.83[YRI][hapmap]
rs655392	0.83[YRI][hapmap]
rs655880	0.83[YRI][hapmap]
rs671353	0.83[YRI][hapmap]
rs686256	0.83[YRI][hapmap]
rs692946	0.83[YRI][hapmap]
rs7027553	0.89[ASN][1000 genomes]
rs7027647	0.87[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7027984	0.87[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7028527	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7039849	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7040866	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7876024	0.87[ASW][hapmap];0.90[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016733	chr9:27073650-27264576	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1022313	chr9:27083369-27250505	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1017802	chr9:27088160-27262682	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1019104	chr9:27088160-27358206	Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv892864	chr9:27176554-27296705	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv466335	chr9:27179244-27234029	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv613946	chr9:27179244-27234029	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1027482	chr9:27195840-27233157	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1018864	chr9:27195840-27294815	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv2761268	chr9:27195852-27291261	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv466336	chr9:27196119-27292703	Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv471294	chr9:27196119-27292703	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv613947	chr9:27196119-27292703	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1033002	chr9:27199373-27232601	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:27151000-27229200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:27165400-27219200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:27166200-27229000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:27180800-27230600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:27184200-27212600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr9:27193000-27209000	Weak transcription	Fetal Stomach	stomach
7	chr9:27193000-27212600	Weak transcription	Spleen	Spleen
8	chr9:27193000-27220000	Weak transcription	Fetal Muscle Leg	muscle
9	chr9:27195200-27221800	Weak transcription	Fetal Intestine Large	intestine
10	chr9:27196800-27228800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr9:27198400-27219800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr9:27198400-27219800	Weak transcription	Ovary	ovary
13	chr9:27201200-27212600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr9:27201400-27224800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:27202400-27220600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr9:27203800-27218600	Weak transcription	Aorta	Aorta
17	chr9:27204600-27207400	Strong transcription	Adipose Nuclei	Adipose
18	chr9:27205000-27217200	Weak transcription	Right Ventricle	heart
19	chr9:27205000-27217600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:27205200-27207400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:27205200-27210000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:27205200-27210200	Weak transcription	Lung	lung
23	chr9:27205400-27206400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:27205400-27209000	Weak transcription	HUVEC	blood vessel
25	chr9:27205800-27206400	Genic enhancers	Left Ventricle	heart
26	chr9:27205800-27207200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr9:27205800-27207400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:27206000-27206400	Enhancers	Psoas Muscle	Psoas

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