Variant report

Variant	rs11168460
Chromosome Location	chr12:48597365-48597366
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	POLR2A	chr12:48595801-48598103	K562	blood:	n/a	n/a
2	POLR2A	chr12:48597210-48597410	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48597340..48600068-chr12:48604806..48607585,2	MCF-7	breast:
2	chr12:48418539..48420191-chr12:48595608..48598283,2	K562	blood:

Variant related genes	Relation type
OR10AD1	TF binding region
ENSG00000257955	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10875743	1.00[CHB][hapmap]
rs10875749	1.00[CHB][hapmap]
rs10875753	1.00[CHB][hapmap]
rs10875763	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1107654	1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168408	1.00[CHB][hapmap]
rs11168428	1.00[CHB][hapmap]
rs11168437	1.00[CHB][hapmap]
rs11168441	1.00[CHB][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs11168464	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168468	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168474	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168484	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12228750	1.00[CHB][hapmap]
rs12368659	1.00[CHB][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs12816820	1.00[CHB][hapmap]
rs12828309	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12829841	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1387259	0.83[EUR][1000 genomes]
rs1387260	0.83[EUR][1000 genomes]
rs1476607	1.00[CHB][hapmap]
rs1542707	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552550	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054905	1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634693	0.80[EUR][1000 genomes]
rs2634697	1.00[ASN][1000 genomes]
rs2732445	1.00[ASN][1000 genomes]
rs2732461	0.82[EUR][1000 genomes]
rs2732462	0.83[EUR][1000 genomes]
rs2956703	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2956710	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087716	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34286639	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760612	1.00[CHB][hapmap]
rs4760679	1.00[CHB][hapmap]
rs6580662	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139330	1.00[CHB][hapmap]
rs7297824	1.00[CHB][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301003	1.00[CHB][hapmap]
rs7307566	1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315820	1.00[CHB][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7486941	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7487682	1.00[CHB][hapmap];0.88[YRI][hapmap]
rs7959684	1.00[CHB][hapmap]
rs7966829	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975632	1.00[CHB][hapmap]
rs8716	1.00[CHB][hapmap]
rs973398	1.00[CHB][hapmap]

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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv976031	chr12:48594968-48610975	Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv976038	chr12:48596152-48610975	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11168460	H1FNT	cis	Muscle Skeletal	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48592800-48600400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:48593200-48599000	Weak transcription	Brain Angular Gyrus	brain
3	chr12:48593200-48600200	Weak transcription	Right Ventricle	heart
4	chr12:48593400-48600800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:48593800-48598400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr12:48593800-48598400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:48594000-48598400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:48594200-48598600	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:48594200-48598800	Weak transcription	Fetal Heart	heart
10	chr12:48594800-48599000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr12:48595000-48598400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:48595000-48598400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:48595200-48597600	Weak transcription	Brain Anterior Caudate	brain
14	chr12:48595200-48598600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:48595200-48598600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:48595200-48598800	Weak transcription	Fetal Lung	lung
17	chr12:48595200-48600400	Weak transcription	Psoas Muscle	Psoas
18	chr12:48595600-48609600	Weak transcription	Placenta	Placenta
19	chr12:48595800-48599600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:48595800-48600800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:48596000-48599600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:48596200-48598400	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr12:48596600-48603800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr12:48596800-48598600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr12:48597000-48598600	Weak transcription	Brain Substantia Nigra	brain
26	chr12:48597000-48606600	Weak transcription	Left Ventricle	heart
27	chr12:48597000-48606800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:48597200-48598400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr12:48597200-48598600	Weak transcription	Gastric	stomach
30	chr12:48597200-48598600	Weak transcription	Ovary	ovary

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