Variant report

Variant	rs3817627
Chromosome Location	chr3:120369575-120369576
allele	A/C
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	chr3:120368290-120370929	HepG2	liver:	n/a	n/a
2	NR2F2	chr3:120369160-120369646	MCF-7	breast:	n/a	n/a
3	GATA3	chr3:120369083-120369659	MCF-7	breast:	n/a	n/a
4	GATA3	chr3:120369011-120369695	MCF-7	breast:	n/a	n/a
5	SIN3AK20	chr3:120369032-120369727	MCF-7	breast:	n/a	n/a
6	EP300	chr3:120369108-120369717	MCF-7	breast:	n/a	chr3:120369377-120369387
7	GATA3	chr3:120369171-120369709	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120360281..120364925-chr3:120365201..120370136,9	K562	blood:

Variant related genes	Relation type
HGD	TF binding region
ENSG00000113924	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs16849176	0.84[CHD][hapmap]
rs1862941	0.88[ASN][1000 genomes]
rs2432696	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2551614	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753090	0.80[MKK][hapmap]
rs726267	0.88[ASN][1000 genomes]
rs7610838	0.95[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	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	esv3373301	chr3:120273762-120421260	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv877377	chr3:120287683-120426750	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	esv3464294	chr3:120303062-120420810	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	esv3464295	chr3:120303062-120420810	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv829699	chr3:120308332-120484695	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
11	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3817627	PARP9	cis	cerebellum	SCAN
rs3817627	GTF2E1	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120346400-120402200	Weak transcription	Gastric	stomach
2	chr3:120347400-120398000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:120355600-120371200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:120355800-120369800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:120356600-120378200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr3:120358600-120369600	Strong transcription	Liver	Liver
7	chr3:120359200-120377600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:120360800-120372200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:120361000-120369600	Weak transcription	Pancreas	Pancrea
10	chr3:120361000-120372000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:120363800-120371800	Weak transcription	Stomach Mucosa	stomach
12	chr3:120366000-120371600	Weak transcription	Fetal Stomach	stomach
13	chr3:120366200-120371200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:120366400-120370000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr3:120367000-120370200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:120367000-120370600	Weak transcription	Fetal Heart	heart
17	chr3:120367600-120371600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:120368200-120369800	Enhancers	Fetal Intestine Small	intestine
19	chr3:120368400-120369600	Enhancers	Ovary	ovary
20	chr3:120368400-120370000	Enhancers	Fetal Intestine Large	intestine
21	chr3:120368400-120370800	Genic enhancers	HepG2	liver
22	chr3:120368800-120369600	Enhancers	A549	lung
23	chr3:120368800-120378200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:120369400-120371000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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