Variant report

Variant	rs12096737
Chromosome Location	chr1:226276554-226276555
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226271544..226273166-chr1:226274162..226276596,2	K562	blood:
2	chr1:226273328..226275664-chr1:226276167..226279764,3	K562	blood:
3	chr1:226269914..226275147-chr1:226275590..226280617,8	MCF-7	breast:
4	chr1:226270119..226272721-chr1:226276429..226280440,3	MCF-7	breast:
5	chr1:226273637..226275167-chr1:226276339..226278999,2	K562	blood:
6	chr1:226276150..226278572-chr1:226296104..226299009,3	MCF-7	breast:
7	chr1:226275598..226277765-chr1:226293845..226296301,2	MCF-7	breast:
8	chr1:226269982..226272748-chr1:226275764..226279082,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000225518	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10753411	0.86[LWK][hapmap];0.84[YRI][hapmap]
rs10799335	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10915930	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10915931	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10915932	0.96[EUR][1000 genomes]
rs12060155	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066979	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12086044	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12096468	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2377470	0.81[ASN][1000 genomes]
rs28737326	0.80[ASN][1000 genomes]
rs3768543	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4012723	0.81[ASN][1000 genomes]
rs4271181	0.95[CEU][hapmap];0.81[CHB][hapmap];0.93[EUR][1000 genomes]
rs61835246	0.84[ASN][1000 genomes]
rs61835247	0.80[ASN][1000 genomes]
rs6426106	0.83[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.80[TSI][hapmap];0.80[ASN][1000 genomes]
rs6678547	0.90[EUR][1000 genomes]
rs6681021	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6692329	0.95[EUR][1000 genomes]
rs6692849	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700189	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7522361	0.83[ASN][1000 genomes]
rs7543135	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12096737	H3F3A	cis	Muscle Skeletal	GTEx
rs12096737	H3F3A	cis	Artery Aorta	GTEx
rs12096737	H3F3A	cis	Artery Tibial	GTEx
rs12096737	H3F3A	cis	Adipose Subcutaneous	GTEx
rs12096737	H3F3A	cis	Esophagus Muscularis	GTEx
rs12096737	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx
rs12096737	H3F3A	cis	Nerve Tibial	GTEx
rs12096737	H3F3A	cis	Esophagus Mucosa	GTEx
rs12096737	H3F3A	cis	Whole Blood	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226271800-226277000	Weak transcription	K562	blood
2	chr1:226271800-226286200	Weak transcription	Ovary	ovary
3	chr1:226271800-226288000	Weak transcription	Right Atrium	heart
4	chr1:226271800-226288400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:226272000-226276800	Weak transcription	Colonic Mucosa	Colon
6	chr1:226272000-226281000	Weak transcription	Fetal Muscle Leg	muscle
7	chr1:226272000-226282200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr1:226272000-226285400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:226272000-226287800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr1:226272000-226288200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:226274800-226279600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:226276400-226276800	Enhancers	Placenta	Placenta

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