Variant report

Variant	rs10875743
Chromosome Location	chr12:48498413-48498414
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HDAC2	chr12:48498347-48498821	MCF-7	breast:	n/a	chr12:48498689-48498703
2	MAX	chr12:48498313-48498768	MCF-7	breast:	n/a	n/a
3	RELA	chr12:48498308-48500398	GM12878	blood:	n/a	chr12:48499466-48499475 chr12:48499466-48499475
4	HCFC1	chr12:48498126-48501600	Hela-S3	cervix:	n/a	n/a
5	NRF1	chr12:48498369-48498561	GM12878	blood:	n/a	n/a
6	GATA3	chr12:48498329-48498678	T-47D	breast:	n/a	n/a
7	GATA3	chr12:48498292-48498831	MCF-7	breast:	n/a	n/a
8	FOXA1	chr12:48498332-48498648	T-47D	breast:	n/a	n/a
9	POLR2A	chr12:48498219-48498732	GM12892	blood:	n/a	n/a
10	ZNF217	chr12:48498360-48498735	MCF-7	breast:	n/a	n/a
11	HDAC2	chr12:48498308-48498820	MCF-7	breast:	n/a	chr12:48498689-48498703
12	WRNIP1	chr12:48498305-48498641	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:48498334-48501462	GM12891	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48497572..48499249-chr12:48549769..48551418,2	MCF-7	breast:
2	chr12:48492802..48495479-chr12:48497432..48499214,2	K562	blood:
3	chr12:48492914..48496557-chr12:48498180..48501677,4	MCF-7	breast:
4	chr12:48496939..48501728-chr12:48549612..48553634,6	MCF-7	breast:
5	chr12:48490196..48492740-chr12:48498056..48500665,3	MCF-7	breast:
6	chr12:48497586..48502171-chr12:48511099..48514258,8	MCF-7	breast:
7	chr12:48495831..48503326-chr12:48548997..48555180,8	K562	blood:
8	chr12:48497262..48501671-chr12:48511273..48513832,5	K562	blood:
9	chr12:48496389..48500489-chr12:48511491..48515053,4	K562	blood:

No data

Variant related genes	Relation type
PFKM	TF binding region
SENP1	TF binding region
ENSG00000258051	Chromatin interaction
ENSG00000152556	Chromatin interaction
ENSG00000177981	Chromatin interaction
ENSG00000079387	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10161358	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10875716	0.88[CEU][hapmap]
rs10875718	0.88[CEU][hapmap]
rs10875719	0.88[CEU][hapmap]
rs10875749	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10875753	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs1107654	1.00[CHB][hapmap]
rs11168351	0.88[CEU][hapmap]
rs11168408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168428	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11168437	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs11168441	1.00[CHB][hapmap]
rs11168460	1.00[CHB][hapmap]
rs12099462	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12228750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12368659	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12816820	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1476607	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17122498	1.00[CHB][hapmap]
rs2051851	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2054905	1.00[CHB][hapmap]
rs3997	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4760612	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.83[EUR][1000 genomes]
rs4760679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6580650	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6580652	0.86[EUR][1000 genomes]
rs6580654	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7139330	1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7295580	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7297824	1.00[CHB][hapmap]
rs7301003	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7307566	1.00[CHB][hapmap]
rs7315820	1.00[CHB][hapmap]
rs7486941	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs7487682	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs7971880	0.88[CEU][hapmap]
rs7975632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs8716	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs973398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9971924	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][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	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	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	esv3384217	chr12:48497934-48498463	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10875743	H1FNT	cis	Muscle Skeletal	GTEx
rs10875743	RP1-228P16.1	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48483200-48499200	Weak transcription	Small Intestine	intestine
2	chr12:48486200-48499000	Weak transcription	Gastric	stomach
3	chr12:48488200-48499200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:48489600-48499000	Weak transcription	Esophagus	oesophagus
5	chr12:48490600-48499000	Weak transcription	Ovary	ovary
6	chr12:48492000-48499000	Weak transcription	Placenta	Placenta
7	chr12:48493600-48498600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:48496600-48500400	Active TSS	GM12878-XiMat	blood
9	chr12:48497600-48498600	Enhancers	Fetal Heart	heart
10	chr12:48497600-48498600	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr12:48498000-48498600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:48498000-48499200	Flanking Active TSS	Dnd41	blood
13	chr12:48498200-48498600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
14	chr12:48498200-48498600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:48498200-48498600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:48498200-48498600	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr12:48498200-48498600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr12:48498200-48498600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:48498200-48498600	Enhancers	Adipose Nuclei	Adipose
20	chr12:48498200-48498600	Enhancers	Colon Smooth Muscle	Colon
21	chr12:48498200-48498600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr12:48498200-48498600	Enhancers	Fetal Intestine Large	intestine
23	chr12:48498200-48498600	Enhancers	Fetal Stomach	stomach
24	chr12:48498200-48498600	Enhancers	Psoas Muscle	Psoas
25	chr12:48498200-48498600	Enhancers	Spleen	Spleen
26	chr12:48498200-48498600	Flanking Active TSS	K562	blood
27	chr12:48498200-48498600	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr12:48498200-48498800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:48498200-48498800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:48498200-48498800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr12:48498200-48498800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr12:48498200-48498800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:48498200-48498800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr12:48498200-48498800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:48498200-48498800	Enhancers	Primary T cells from cord blood	blood
36	chr12:48498200-48498800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr12:48498200-48498800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:48498200-48498800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:48498200-48498800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:48498200-48498800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:48498200-48498800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:48498200-48498800	Enhancers	Pancreas	Pancrea
43	chr12:48498200-48498800	Flanking Active TSS	A549	lung
44	chr12:48498200-48498800	Flanking Active TSS	HepG2	liver
45	chr12:48498200-48498800	Flanking Active TSS	HMEC	breast
46	chr12:48498200-48498800	Flanking Active TSS	NH-A	brain
47	chr12:48498200-48498800	Flanking Active TSS	NHLF	lung
48	chr12:48498200-48499000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:48498200-48499000	Enhancers	Primary B cells from peripheral blood	blood
50	chr12:48498200-48499000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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