Variant report

Variant	rs1370062
Chromosome Location	chr15:31527759-31527760
allele	C/T
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	USF2	chr15:31527694-31528102	GM12878	blood:	n/a	n/a
2	CHD2	chr15:31527753-31529285	GM12878	blood:	n/a	n/a
3	RUNX3	chr15:31527622-31529044	GM12878	blood:	n/a	n/a
4	EP300	chr15:31527461-31530109	SK-N-SH	brain:	n/a	chr15:31528940-31528949 chr15:31529219-31529233 chr15:31528648-31528664 chr15:31528941-31528950 chr15:31529680-31529694 chr15:31529839-31529848 chr15:31528393-31528407
5	EBF1	chr15:31527719-31529073	GM12878	blood:	n/a	n/a
6	MTA3	chr15:31527705-31528980	GM12878	blood:	n/a	n/a
7	GATA3	chr15:31527635-31528744	SH-SY5Y	brain:	n/a	chr15:31527748-31527760 chr15:31528130-31528140 chr15:31528395-31528405
8	EP300	chr15:31527739-31529436	GM12878	blood:	n/a	chr15:31528940-31528949 chr15:31529219-31529233 chr15:31528648-31528664 chr15:31528941-31528950 chr15:31528393-31528407
9	RELA	chr15:31527737-31529150	GM10847	blood:	n/a	n/a
10	NFIC	chr15:31527719-31529061	GM12878	blood:	n/a	chr15:31528207-31528224
11	POLR2A	chr15:31527623-31528858	GM12878	blood:	n/a	n/a
12	EP300	chr15:31527751-31528394	SK-N-SH_RA	brain:	n/a	n/a
13	BHLHE40	chr15:31527467-31528988	GM12878	blood:	n/a	n/a
14	JUND	chr15:31527537-31530077	SK-N-SH	brain:	n/a	chr15:31528939-31528950 chr15:31529854-31529863 chr15:31528942-31528949 chr15:31528489-31528501 chr15:31528939-31528951 chr15:31528941-31528949 chr15:31528941-31528950
15	NFIC	chr15:31527738-31529293	SK-N-SH	brain:	n/a	chr15:31528207-31528224
16	ZNF263	chr15:31527751-31528557	HEK293-T-REx	kidney:	n/a	chr15:31528236-31528245
17	GATA2	chr15:31527538-31529229	SH-SY5Y	brain:	n/a	chr15:31528939-31528948 chr15:31528942-31528951 chr15:31527748-31527760 chr15:31528130-31528140 chr15:31528395-31528405
18	GATA1	chr15:31527675-31528609	PBDE	blood:	n/a	chr15:31527748-31527760 chr15:31528130-31528140 chr15:31528395-31528405
19	MXI1	chr15:31527647-31528862	GM12878	blood:	n/a	n/a
20	BHLHE40	chr15:31527666-31527889	K562	blood:	n/a	n/a
21	MAX	chr15:31527601-31528887	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000259772	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10438322	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12101670	1.00[ASN][1000 genomes]
rs12437996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12438318	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs12439686	0.89[ASN][1000 genomes]
rs16956707	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs1972825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28631253	0.97[ASN][1000 genomes]
rs28669757	0.97[ASN][1000 genomes]
rs3743235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6493531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6493532	0.94[AMR][1000 genomes]
rs7162278	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7162751	0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs754611	0.96[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9944280	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS 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	87 gene(s)	inside rSNPs	diseases
5	nsv1036018	chr15:31140415-31544888	Enhancers Flanking Active TSS Active TSS Genic 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 miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv1052722	chr15:31261834-31609680	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv542315	chr15:31261834-31609680	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
9	nsv903838	chr15:31452911-31672128	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	esv1815415	chr15:31483843-31697213	Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
11	nsv903839	chr15:31495113-31576677	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	esv34100	chr15:31496514-31792591	Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1370062	CHRFAM7A	cis	multi-tissue	Pritchard

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31518400-31540600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:31520800-31533600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr15:31521400-31528600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:31521800-31527800	Weak transcription	Gastric	stomach
5	chr15:31522000-31527800	Weak transcription	Stomach Mucosa	stomach
6	chr15:31523000-31529600	Enhancers	Primary B cells from peripheral blood	blood
7	chr15:31523800-31528000	Weak transcription	Esophagus	oesophagus
8	chr15:31524200-31527800	Weak transcription	Lung	lung
9	chr15:31524200-31528600	Weak transcription	Thymus	Thymus
10	chr15:31524200-31533400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:31524600-31528400	Enhancers	Fetal Heart	heart
12	chr15:31525200-31528200	Enhancers	Brain Germinal Matrix	brain
13	chr15:31525200-31532000	Enhancers	Fetal Thymus	thymus
14	chr15:31525400-31529800	Enhancers	Right Ventricle	heart
15	chr15:31525600-31527800	Weak transcription	Right Atrium	heart
16	chr15:31525800-31530600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr15:31526200-31527800	Weak transcription	Fetal Brain Male	brain
18	chr15:31526400-31527800	Weak transcription	Spleen	Spleen
19	chr15:31526400-31529800	Enhancers	Left Ventricle	heart
20	chr15:31526600-31528000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr15:31526800-31529000	Enhancers	Primary B cells from cord blood	blood
22	chr15:31527000-31527800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:31527000-31532200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr15:31527200-31527800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr15:31527200-31529800	Enhancers	Fetal Intestine Small	intestine
26	chr15:31527400-31529600	Enhancers	Fetal Muscle Trunk	muscle
27	chr15:31527400-31529800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:31527400-31532200	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr15:31527600-31528200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:31527600-31528200	Flanking Active TSS	GM12878-XiMat	blood
31	chr15:31527600-31528400	Enhancers	Stomach Smooth Muscle	stomach
32	chr15:31527600-31528600	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr15:31527600-31528800	Enhancers	Adipose Nuclei	Adipose
34	chr15:31527600-31529600	Enhancers	Duodenum Mucosa	Duodenum
35	chr15:31527600-31529800	Enhancers	Rectal Smooth Muscle	rectum
36	chr15:31527600-31530000	Enhancers	Fetal Stomach	stomach

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