Variant report

Variant	rs12378286
Chromosome Location	chr9:21536397-21536398
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10491567	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10811535	0.82[CEU][hapmap]
rs10811549	0.89[EUR][1000 genomes]
rs10811551	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs10811556	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10811557	1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs10811562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10811563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10811564	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10811565	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10811566	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10811568	0.93[ASN][1000 genomes]
rs10964981	1.00[CEU][hapmap]
rs10964982	0.82[CEU][hapmap]
rs10964985	1.00[CEU][hapmap]
rs10965002	1.00[CEU][hapmap]
rs10965005	0.82[CEU][hapmap]
rs10965008	1.00[CEU][hapmap]
rs10965019	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs10965024	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs10965031	0.87[EUR][1000 genomes]
rs10965034	0.82[EUR][1000 genomes]
rs10965036	0.82[EUR][1000 genomes]
rs10965049	0.86[CHB][hapmap];0.95[ASN][1000 genomes]
rs10965050	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10965053	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10965054	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10965059	0.95[EUR][1000 genomes]
rs10965060	0.84[ASN][1000 genomes]
rs10965063	0.89[EUR][1000 genomes]
rs1125488	0.84[EUR][1000 genomes]
rs12375583	0.82[EUR][1000 genomes]
rs12377379	0.95[EUR][1000 genomes]
rs12378990	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12379382	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12379709	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12379721	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1332188	0.82[EUR][1000 genomes]
rs16938384	0.82[CEU][hapmap]
rs16938433	0.82[EUR][1000 genomes]
rs16938435	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16938448	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2039380	0.85[EUR][1000 genomes]
rs55683539	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55835613	0.95[EUR][1000 genomes]
rs56122777	0.95[EUR][1000 genomes]
rs56337511	0.82[EUR][1000 genomes]
rs7026731	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7032680	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7034161	1.00[CEU][hapmap]
rs7041183	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72703410	0.80[EUR][1000 genomes]
rs72703411	0.87[EUR][1000 genomes]
rs72703417	0.82[EUR][1000 genomes]
rs72703418	0.82[EUR][1000 genomes]
rs72703419	0.82[EUR][1000 genomes]
rs72703426	0.82[EUR][1000 genomes]
rs72703442	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs72703445	0.95[EUR][1000 genomes]
rs72703447	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72703448	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72703449	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72703450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7861480	0.82[CEU][hapmap]
rs9644855	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[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	nsv892740	chr9:21471499-21551513	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA	110 gene(s)	inside rSNPs	diseases
2	nsv1031432	chr9:21472601-21608774	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
3	nsv540085	chr9:21472601-21608774	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
4	nsv892741	chr9:21517302-21551513	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21507200-21551400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:21508000-21542000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:21516800-21542600	Weak transcription	Stomach Mucosa	stomach
4	chr9:21527800-21536600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:21528800-21542000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:21529000-21551400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:21531600-21542600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr9:21532200-21542800	Weak transcription	NHLF	lung
9	chr9:21532400-21542000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:21533200-21542600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr9:21534000-21542000	Weak transcription	HUVEC	blood vessel
12	chr9:21534000-21543000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:21534000-21544200	Weak transcription	NHDF-Ad	bronchial
14	chr9:21534400-21548200	Weak transcription	HSMM	muscle
15	chr9:21534800-21536400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr9:21534800-21536800	Genic enhancers	NHEK	skin
17	chr9:21535000-21536400	Strong transcription	Hela-S3	cervix
18	chr9:21535000-21536400	Genic enhancers	Osteobl	bone
19	chr9:21535000-21536600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:21535000-21536800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:21535200-21536600	Genic enhancers	HMEC	breast
22	chr9:21535200-21536800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr9:21535200-21537400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr9:21535400-21536600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:21535600-21542000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:21535800-21536400	Enhancers	Gastric	stomach
27	chr9:21535800-21536600	Genic enhancers	A549	lung
28	chr9:21536000-21536600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:21536000-21543000	Weak transcription	NH-A	brain
30	chr9:21536200-21536400	ZNF genes & repeats	Fetal Intestine Small	intestine
31	chr9:21536200-21542200	Weak transcription	Muscle Satellite Cultured Cells	--

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