Variant report

Variant	rs1025690
Chromosome Location	chr3:53882663-53882664
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	EBF1	chr3:53882619-53882840	GM12878	blood:	n/a	n/a
2	BHLHE40	chr3:53882631-53882725	GM12878	blood:	n/a	n/a
3	ZNF384	chr3:53882560-53882763	GM12878	blood:	n/a	chr3:53882672-53882680
4	POLR2A	chr3:53881915-53884827	HepG2	liver:	n/a	n/a
5	EP300	chr3:53882611-53882730	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53882268..53884684-chr3:53906455..53909246,2	MCF-7	breast:
2	chr3:53882366..53883990-chr3:53889340..53891284,2	MCF-7	breast:

Variant related genes	Relation type
CHDH	TF binding region
ENSG00000113812	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1025689	0.87[CEU][hapmap]
rs17641133	0.92[EUR][1000 genomes]
rs2118421	0.92[EUR][1000 genomes]
rs2232332	0.97[ASN][1000 genomes]
rs2232333	0.94[EUR][1000 genomes]
rs2276839	0.83[CEU][hapmap];0.92[EUR][1000 genomes]
rs2289205	0.86[EUR][1000 genomes]
rs2884632	0.95[ASN][1000 genomes]
rs3755817	0.86[EUR][1000 genomes]
rs4546140	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs45560831	0.92[EUR][1000 genomes]
rs45616236	0.92[EUR][1000 genomes]
rs4687751	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs55754695	0.82[EUR][1000 genomes]
rs55974100	0.89[EUR][1000 genomes]
rs56052250	0.88[EUR][1000 genomes]
rs7627178	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs7650883	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876803	chr3:53822893-53889849	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv518466	chr3:53832903-53882663	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv876805	chr3:53865731-53883722	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised 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	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1025690	ACTR8	cis	cerebellum	SCAN
rs1025690	RASSF1	cis	cerebellum	SCAN
rs1025690	DCP1A	cis	lymphoblastoid	seeQTL
rs1025690	IL17RB	cis	cerebellum	SCAN
rs1025690	SEMA3G	cis	parietal	SCAN
rs1025690	PHF7	cis	parietal	SCAN
rs1025690	ACTR8	cis	parietal	SCAN
rs1025690	CACNA1D	cis	cerebellum	SCAN
rs1025690	ABHD14A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53881000-53885200	Weak transcription	Right Atrium	heart
2	chr3:53881000-53892600	Weak transcription	Psoas Muscle	Psoas
3	chr3:53881000-53893200	Weak transcription	Ovary	ovary
4	chr3:53881200-53892400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:53881200-53895000	Weak transcription	A549	lung
6	chr3:53881200-53895800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:53881400-53886600	Weak transcription	Brain Substantia Nigra	brain
8	chr3:53881400-53887000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:53881400-53887200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:53881400-53887400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:53881400-53889200	Weak transcription	Fetal Intestine Small	intestine
12	chr3:53881400-53891400	Weak transcription	Brain Anterior Caudate	brain
13	chr3:53881400-53892000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:53881400-53892000	Weak transcription	Gastric	stomach
15	chr3:53881400-53892200	Weak transcription	Fetal Intestine Large	intestine
16	chr3:53881400-53892200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:53881400-53892600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:53881400-53892600	Weak transcription	Hela-S3	cervix
19	chr3:53881400-53892800	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:53881400-53893000	Weak transcription	Brain Angular Gyrus	brain
21	chr3:53881400-53893000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr3:53881600-53887000	Weak transcription	Liver	Liver
23	chr3:53882200-53882800	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr3:53882400-53883200	Enhancers	Pancreas	Pancrea
25	chr3:53882400-53883200	Transcr. at gene 5' and 3'	HepG2	liver
26	chr3:53882400-53883600	Weak transcription	Stomach Mucosa	stomach
27	chr3:53882400-53886800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:53882400-53891400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:53882600-53882800	Active TSS	GM12878-XiMat	blood
30	chr3:53882600-53886200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr3:53882600-53892200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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