Variant report

Variant	rs3773717
Chromosome Location	chr3:156272292-156272293
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	POLR2A	chr3:156271592-156273408	HUVEC	blood vessel:	n/a	n/a
2	MYC	chr3:156271575-156273303	K562	blood:	n/a	chr3:156271916-156271923 chr3:156273112-156273121 chr3:156273110-156273123 chr3:156273110-156273123 chr3:156273110-156273118 chr3:156273110-156273123 chr3:156273112-156273121 chr3:156273111-156273122 chr3:156273271-156273280 chr3:156271915-156271924
3	MYC	chr3:156271711-156273321	K562	blood:	n/a	chr3:156271916-156271923 chr3:156273112-156273121 chr3:156273110-156273123 chr3:156273110-156273123 chr3:156273110-156273118 chr3:156273110-156273123 chr3:156273112-156273121 chr3:156273111-156273122 chr3:156273271-156273280 chr3:156271915-156271924
4	MAX	chr3:156271545-156272299	A549	lung:	n/a	chr3:156271916-156271923 chr3:156271915-156271924
5	BHLHE40	chr3:156271773-156273471	GM12878	blood:	n/a	chr3:156272945-156272961
6	CEBPB	chr3:156271516-156273211	Hela-S3	cervix:	n/a	chr3:156271682-156271693 chr3:156271681-156271694 chr3:156272271-156272282 chr3:156272271-156272284 chr3:156271681-156271692 chr3:156272271-156272282 chr3:156271681-156271694 chr3:156272271-156272284
7	MAX	chr3:156271698-156273375	Hela-S3	cervix:	n/a	chr3:156271916-156271923 chr3:156273112-156273121 chr3:156273110-156273123 chr3:156273110-156273123 chr3:156273110-156273118 chr3:156273110-156273123 chr3:156273112-156273121 chr3:156273111-156273122 chr3:156273271-156273280 chr3:156271915-156271924
8	CEBPB	chr3:156271505-156272584	K562	blood:	n/a	chr3:156271682-156271693 chr3:156271681-156271694 chr3:156272271-156272282 chr3:156272271-156272284 chr3:156271681-156271692 chr3:156272271-156272282 chr3:156271681-156271694 chr3:156272271-156272284
9	SREBP1	chr3:156271429-156274240	GM12878	blood:	n/a	n/a
10	MXI1	chr3:156271033-156273803	IMR90	lung:	n/a	chr3:156273113-156273122
11	MYC	chr3:156271532-156273382	K562	blood:	n/a	chr3:156271916-156271923 chr3:156273112-156273121 chr3:156273110-156273123 chr3:156273110-156273123 chr3:156273110-156273118 chr3:156273110-156273123 chr3:156273112-156273121 chr3:156273111-156273122 chr3:156273271-156273280 chr3:156271915-156271924
12	MYC	chr3:156271267-156272427	MCF10A-Er-Src	breast:	n/a	chr3:156271916-156271923 chr3:156271915-156271924
13	SIN3AK20	chr3:156271612-156273644	MCF-7	breast:	n/a	n/a
14	POLR2A	chr3:156271941-156272322	GM12878	blood:	n/a	n/a
15	MXI1	chr3:156271443-156273802	SK-N-SH	brain:	n/a	chr3:156273113-156273122
16	HEY1	chr3:156271783-156272335	K562	blood:	n/a	n/a
17	CHD1	chr3:156272057-156273401	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr3:156272085-156273421	MCF10A-Er-Src	breast:	n/a	n/a
19	CUX1	chr3:156271660-156272343	K562	blood:	n/a	n/a
20	HCFC1	chr3:156271011-156273637	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr3:156271487-156273100	HepG2	liver:	n/a	n/a
22	WRNIP1	chr3:156271850-156273460	GM12878	blood:	n/a	n/a
23	MXI1	chr3:156271580-156273420	GM12878	blood:	n/a	chr3:156273113-156273122
24	POLR2A	chr3:156271748-156273454	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:156271486-156273320	IMR90	lung:	n/a	n/a
26	CEBPB	chr3:156272210-156272459	H1-hESC	embryonic stem cell:	n/a	chr3:156272271-156272282 chr3:156272271-156272284 chr3:156272271-156272282 chr3:156272271-156272284
27	POLR2A	chr3:156272259-156273200	ProgFib	skin:	n/a	n/a
28	CEBPB	chr3:156271530-156272448	IMR90	lung:	n/a	chr3:156271682-156271693 chr3:156271681-156271694 chr3:156272271-156272282 chr3:156272271-156272284 chr3:156271681-156271692 chr3:156272271-156272282 chr3:156271681-156271694 chr3:156272271-156272284
29	MXI1	chr3:156272291-156273310	K562	blood:	n/a	chr3:156273113-156273122
30	IRF1	chr3:156271563-156272478	K562	blood:	n/a	chr3:156272049-156272059
31	YY1	chr3:156272246-156273575	SK-N-SH	brain:	n/a	chr3:156272946-156272957 chr3:156272985-156272999
32	MTA3	chr3:156272250-156273536	GM12878	blood:	n/a	n/a
33	POLR2A	chr3:156272172-156273117	K562	blood:	n/a	n/a
34	POLR2A	chr3:156271558-156273013	HepG2	liver:	n/a	n/a
35	USF2	chr3:156271763-156272314	K562	blood:	n/a	n/a
36	MAX	chr3:156271629-156272303	HCT-116	colon:	n/a	chr3:156271916-156271923 chr3:156271915-156271924
37	RFX5	chr3:156271579-156273517	Hela-S3	cervix:	n/a	n/a
38	SIN3A	chr3:156271829-156273376	H1-hESC	embryonic stem cell:	n/a	chr3:156273113-156273122 chr3:156272690-156272701 chr3:156273111-156273120 chr3:156272641-156272654
39	EP300	chr3:156271996-156272301	GM12878	blood:	n/a	chr3:156272269-156272283
40	POLR2A	chr3:156271617-156273433	GM12878	blood:	n/a	n/a
41	POLR2A	chr3:156271801-156273008	HUVEC	blood vessel:	n/a	n/a
42	POLR2A	chr3:156271978-156273159	HepG2	liver:	n/a	n/a
43	CEBPB	chr3:156271582-156272395	A549	lung:	n/a	chr3:156271682-156271693 chr3:156271681-156271694 chr3:156272271-156272282 chr3:156272271-156272284 chr3:156271681-156271692 chr3:156272271-156272282 chr3:156271681-156271694 chr3:156272271-156272284
44	POLR2A	chr3:156271829-156273687	H1-hESC	embryonic stem cell:	n/a	n/a
45	MAX	chr3:156271584-156273623	HCT-116	colon:	n/a	chr3:156271916-156271923 chr3:156273112-156273121 chr3:156273110-156273123 chr3:156273110-156273123 chr3:156273110-156273118 chr3:156273110-156273123 chr3:156273112-156273121 chr3:156273111-156273122 chr3:156273271-156273280 chr3:156271915-156271924
46	RFX5	chr3:156271883-156272326	HepG2	liver:	n/a	n/a
47	MAX	chr3:156271620-156272315	SK-N-SH	brain:	n/a	chr3:156271916-156271923 chr3:156271915-156271924
48	BHLHE40	chr3:156271784-156272428	HepG2	liver:	n/a	n/a
49	POLR2A	chr3:156271504-156273367	GM12891	blood:	n/a	n/a
50	MAFK	chr3:156271688-156272316	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:156268357..156274553-chr3:156389283..156394606,15	MCF-7	breast:
2	chr3:156271607..156273392-chr3:156891262..156894145,2	K562	blood:
3	chr3:156260735..156275674-chr3:156389736..156397850,44	K562	blood:
4	chr3:156270403..156273229-chr3:156876136..156878579,3	K562	blood:
5	chr3:156271311..156273163-chr3:156875258..156877901,2	MCF-7	breast:
6	chr3:156268894..156273100-chr3:156541711..156545313,4	MCF-7	breast:
7	chr3:156270771..156274735-chr3:156390391..156394038,18	K562	blood:
8	chr3:156270417..156272669-chr3:156876892..156879496,3	MCF-7	breast:
9	chr3:156269857..156276442-chr3:156389324..156394083,11	MCF-7	breast:

Variant related genes	Relation type
SSR3	TF binding region
ENSG00000197980	Chromatin interaction
ENSG00000243926	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000222675	Chromatin interaction
ENSG00000243176	Chromatin interaction
ENSG00000163660	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10936027	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11710396	0.90[ASN][1000 genomes]
rs13068904	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13083246	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13088140	1.00[CEU][hapmap]
rs13097501	1.00[CEU][hapmap]
rs17354147	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2874390	1.00[ASN][1000 genomes]
rs3773719	1.00[ASN][1000 genomes]
rs4257505	1.00[CEU][hapmap]
rs6764265	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6764992	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6771728	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802811	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71310479	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71310481	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs756335	1.00[CEU][hapmap]
rs9837799	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917691	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv829764	chr3:156174824-156347774	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
3	nsv877683	chr3:156180366-156272351	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3773717	SSR3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156268200-156273400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:156270600-156273400	Active TSS	HSMMtube	muscle
3	chr3:156270800-156272400	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr3:156270800-156273800	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr3:156271000-156272400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr3:156271000-156273400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:156271000-156273400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:156271000-156273400	Active TSS	Left Ventricle	heart
9	chr3:156271000-156273400	Active TSS	Right Atrium	heart
10	chr3:156271000-156273400	Active TSS	Right Ventricle	heart
11	chr3:156271000-156273400	Active TSS	A549	lung
12	chr3:156271000-156273400	Active TSS	HMEC	breast
13	chr3:156271000-156273600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:156271000-156273600	Active TSS	Aorta	Aorta
15	chr3:156271000-156273600	Active TSS	Ovary	ovary
16	chr3:156271000-156273800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:156271200-156272400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:156271200-156273400	Active TSS	NHLF	lung
19	chr3:156271200-156273600	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr3:156271200-156273600	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr3:156271200-156273600	Active TSS	Psoas Muscle	Psoas
22	chr3:156271200-156273800	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr3:156271200-156273800	Active TSS	GM12878-XiMat	blood
24	chr3:156271400-156272400	Flanking Active TSS	Primary T cells from cord blood	blood
25	chr3:156271400-156272400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:156271400-156272400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr3:156271400-156272400	Flanking Active TSS	Brain Cingulate Gyrus	brain
28	chr3:156271400-156272400	Flanking Active TSS	Fetal Brain Female	brain
29	chr3:156271400-156272600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:156271400-156273200	Active TSS	Fetal Muscle Leg	muscle
31	chr3:156271400-156273400	Active TSS	H1 Cell Line	embryonic stem cell
32	chr3:156271400-156273400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:156271400-156273600	Active TSS	Colonic Mucosa	Colon
34	chr3:156271600-156272400	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr3:156271600-156272400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr3:156271600-156272400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
37	chr3:156271600-156272400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr3:156271600-156272800	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr3:156271600-156272800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:156271600-156273200	Active TSS	Muscle Satellite Cultured Cells	--
41	chr3:156271600-156273200	Active TSS	Rectal Smooth Muscle	rectum
42	chr3:156271600-156273200	Active TSS	NH-A	brain
43	chr3:156271600-156273400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:156271600-156273400	Active TSS	Fetal Intestine Large	intestine
45	chr3:156271600-156273400	Active TSS	NHDF-Ad	bronchial
46	chr3:156271600-156273600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr3:156271600-156273600	Active TSS	H9 Cell Line	embryonic stem cell
48	chr3:156271600-156273600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:156271600-156273800	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr3:156271600-156273800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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