Variant report

Variant	rs6445607
Chromosome Location	chr3:53877149-53877150
allele	G/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	MAX	chr3:53876760-53877192	MCF-7	breast:	n/a	n/a
2	FOXA1	chr3:53876887-53877258	T-47D	breast:	n/a	n/a
3	REST	chr3:53876715-53877740	HepG2	liver:	n/a	chr3:53876875-53876895 chr3:53876909-53876922 chr3:53876879-53876892 chr3:53876909-53876922
4	WRNIP1	chr3:53876871-53878169	GM12878	blood:	n/a	n/a
5	FOXA2	chr3:53876736-53877673	HepG2	liver:	n/a	n/a
6	RELA	chr3:53876863-53878419	GM19099	blood:	n/a	chr3:53877197-53877206 chr3:53878032-53878041 chr3:53877197-53877206 chr3:53878032-53878041
7	FOXA1	chr3:53876281-53877784	HepG2	liver:	n/a	n/a
8	MYC	chr3:53876850-53877212	HepG2	liver:	n/a	n/a
9	MAFK	chr3:53876655-53877220	HepG2	liver:	n/a	n/a
10	SIN3AK20	chr3:53876782-53877200	HepG2	liver:	n/a	n/a
11	RXRA	chr3:53876797-53877773	HepG2	liver:	n/a	chr3:53877568-53877582 chr3:53877567-53877576
12	RELA	chr3:53876706-53878542	GM12891	blood:	n/a	chr3:53878475-53878484 chr3:53877197-53877206 chr3:53878475-53878484 chr3:53878032-53878041 chr3:53877197-53877206 chr3:53878032-53878041
13	FOXA2	chr3:53876894-53877215	A549	lung:	n/a	n/a
14	EP300	chr3:53876690-53877976	HepG2	liver:	n/a	chr3:53877595-53877604 chr3:53877216-53877230 chr3:53877217-53877231
15	HEY1	chr3:53876036-53880070	HepG2	liver:	n/a	n/a
16	HEY1	chr3:53876129-53880020	HepG2	liver:	n/a	n/a
17	HNF4A	chr3:53876697-53878028	HepG2	liver:	n/a	chr3:53877532-53877547 chr3:53877568-53877581 chr3:53877568-53877581 chr3:53877568-53877580 chr3:53877567-53877580 chr3:53877568-53877581 chr3:53877799-53877813 chr3:53877565-53877583 chr3:53877568-53877580 chr3:53877567-53877581 chr3:53877566-53877581 chr3:53877568-53877580 chr3:53877567-53877581 chr3:53877799-53877813 chr3:53877567-53877581 chr3:53877568-53877580 chr3:53877136-53877150
18	HNF4G	chr3:53876740-53878019	HepG2	liver:	n/a	chr3:53877532-53877547 chr3:53877568-53877581 chr3:53877568-53877581 chr3:53877568-53877580 chr3:53877567-53877580 chr3:53877568-53877581 chr3:53877799-53877813 chr3:53877565-53877583 chr3:53877568-53877580 chr3:53877567-53877581 chr3:53877568-53877580 chr3:53877567-53877581 chr3:53877799-53877813 chr3:53877567-53877581 chr3:53877568-53877580 chr3:53877136-53877150
19	POLR2A	chr3:53876086-53880024	HepG2	liver:	n/a	n/a
20	RELA	chr3:53876775-53878205	GM12878	blood:	n/a	chr3:53877197-53877206 chr3:53878032-53878041 chr3:53877197-53877206 chr3:53878032-53878041
21	FOXA1	chr3:53876683-53877521	HepG2	liver:	n/a	n/a
22	CEBPD	chr3:53876789-53877212	HepG2	liver:	n/a	n/a
23	ZNF263	chr3:53876444-53877221	HEK293-T-REx	kidney:	n/a	chr3:53876907-53876928
24	MAX	chr3:53876216-53877795	HepG2	liver:	n/a	n/a
25	SP1	chr3:53876452-53877907	HepG2	liver:	n/a	chr3:53877064-53877078
26	EP300	chr3:53876734-53877804	HepG2	liver:	n/a	chr3:53877595-53877604 chr3:53877216-53877230 chr3:53877217-53877231
27	ARID3A	chr3:53876698-53878019	HepG2	liver:	n/a	chr3:53877014-53877030
28	POLR2A	chr3:53876459-53880951	HepG2	liver:	n/a	n/a
29	SP1	chr3:53876758-53877299	H1-hESC	embryonic stem cell:	n/a	chr3:53877064-53877078
30	MAZ	chr3:53876750-53877808	HepG2	liver:	n/a	n/a
31	HNF4A	chr3:53876732-53877830	HepG2	liver:	n/a	chr3:53877532-53877547 chr3:53877568-53877581 chr3:53877568-53877581 chr3:53877568-53877580 chr3:53877567-53877580 chr3:53877568-53877581 chr3:53877799-53877813 chr3:53877565-53877583 chr3:53877568-53877580 chr3:53877567-53877581 chr3:53877566-53877581 chr3:53877568-53877580 chr3:53877567-53877581 chr3:53877799-53877813 chr3:53877567-53877581 chr3:53877568-53877580 chr3:53877136-53877150
32	FOXA1	chr3:53876845-53877176	T-47D	breast:	n/a	n/a
33	JUND	chr3:53876775-53877328	HepG2	liver:	n/a	n/a
34	HDAC2	chr3:53876695-53877874	HepG2	liver:	n/a	chr3:53877218-53877232 chr3:53877217-53877231 chr3:53877215-53877229 chr3:53876903-53876922 chr3:53877216-53877230
35	POLR2A	chr3:53875240-53880984	HepG2	liver:	n/a	n/a
36	POLR2A	chr3:53876725-53878869	GM19099	blood:	n/a	n/a
37	TAF1	chr3:53876720-53877200	HepG2	liver:	n/a	n/a
38	MAZ	chr3:53877126-53877208	GM12878	blood:	n/a	n/a
39	NFIC	chr3:53876665-53877192	ECC-1	luminal epithelium:	n/a	n/a
40	RCOR1	chr3:53877008-53877428	GM12878	blood:	n/a	n/a
41	MBD4	chr3:53876588-53878155	HepG2	liver:	n/a	n/a
42	TBP	chr3:53876985-53877303	GM12878	blood:	n/a	n/a
43	NR2F2	chr3:53876713-53878089	HepG2	liver:	n/a	chr3:53877564-53877579
44	NFIC	chr3:53876378-53877947	HepG2	liver:	n/a	n/a
45	RAD21	chr3:53876712-53877156	HepG2	liver:	n/a	n/a
46	BRCA1	chr3:53876900-53877389	HepG2	liver:	n/a	n/a
47	CEBPB	chr3:53876851-53877764	HepG2	liver:	n/a	n/a
48	EBF1	chr3:53876510-53878643	GM12878	blood:	n/a	chr3:53878322-53878332 chr3:53877615-53877624 chr3:53877975-53877986 chr3:53878323-53878332
49	EP300	chr3:53876992-53877476	GM12878	blood:	n/a	chr3:53877216-53877230 chr3:53877217-53877231
50	STAT1	chr3:53876971-53877158	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53871494..53874275-chr3:53875042..53877358,2	MCF-7	breast:
2	chr3:53874777..53878635-chr3:53878874..53882397,7	MCF-7	breast:

Variant related genes	Relation type
IL17RB	TF binding region
ENSG00000016391	Chromatin interaction
ENSG00000056736	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11718497	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs35518479	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4687750	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4687751	0.80[CEU][hapmap];0.80[TSI][hapmap]
rs6445608	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6801605	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7627178	0.80[CEU][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs930367	0.89[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs9881815	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv1003204	chr3:53820070-53877149	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv521181	chr3:53833509-53881471	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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
13	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6445607	ACTR8	cis	parietal	SCAN
rs6445607	CACNA1D	cis	cerebellum	SCAN
rs6445607	IL17RB	cis	multi-tissue	Pritchard
rs6445607	ACTR8	cis	cerebellum	SCAN
rs6445607	IL17RB	cis	cerebellum	SCAN
rs6445607	ABHD14A	cis	parietal	SCAN
rs6445607	CHDH	cis	Nerve Tibial	GTEx
rs6445607	IL17RB	cis	Nerve Tibial	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53846600-53879800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:53852400-53878200	Weak transcription	Hela-S3	cervix
3	chr3:53853400-53877200	Weak transcription	Colonic Mucosa	Colon
4	chr3:53853800-53879000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:53854000-53879400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:53854200-53877400	Weak transcription	Esophagus	oesophagus
7	chr3:53856800-53879200	Weak transcription	Ovary	ovary
8	chr3:53865600-53879800	Weak transcription	Aorta	Aorta
9	chr3:53869600-53879600	Weak transcription	Right Atrium	heart
10	chr3:53870200-53878600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:53870800-53879600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:53872800-53877400	Weak transcription	Small Intestine	intestine
13	chr3:53874800-53878000	Enhancers	Fetal Intestine Large	intestine
14	chr3:53875200-53877400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr3:53875200-53877400	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr3:53875200-53878400	Enhancers	Pancreas	Pancrea
17	chr3:53875200-53878600	Enhancers	Stomach Mucosa	stomach
18	chr3:53875200-53879200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:53875200-53879400	Enhancers	H1 Cell Line	embryonic stem cell
20	chr3:53875400-53878600	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr3:53875400-53878800	Enhancers	Brain Hippocampus Middle	brain
22	chr3:53875600-53878000	Weak transcription	Gastric	stomach
23	chr3:53875600-53879000	Enhancers	Fetal Intestine Small	intestine
24	chr3:53875600-53879200	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr3:53875600-53879200	Enhancers	Brain Anterior Caudate	brain
26	chr3:53876200-53878600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:53876200-53878600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:53876200-53879200	Enhancers	Brain Angular Gyrus	brain
29	chr3:53876200-53879600	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr3:53876400-53877600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:53876400-53877600	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr3:53876400-53878200	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr3:53876400-53878200	Flanking Active TSS	GM12878-XiMat	blood
34	chr3:53876400-53878800	Enhancers	Brain Cingulate Gyrus	brain
35	chr3:53876400-53878800	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr3:53876400-53879000	Enhancers	Brain Substantia Nigra	brain
37	chr3:53876400-53879200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:53876400-53879200	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr3:53876400-53879200	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr3:53876400-53879200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:53876400-53879400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:53876600-53877200	Enhancers	NH-A	brain
43	chr3:53876600-53877400	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr3:53876600-53877600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:53876600-53877600	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr3:53876600-53877600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:53876600-53877600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:53876600-53877800	Enhancers	A549	lung
49	chr3:53876600-53878200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:53876600-53879600	Enhancers	Lung	lung

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