Variant report

Variant	rs9880846
Chromosome Location	chr3:61237223-61237224
allele	C/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	TBL1XR1	chr3:61237024-61237437	K562	blood:	n/a	n/a
2	MAX	chr3:61235476-61237558	HCT-116	colon:	n/a	chr3:61236542-61236553 chr3:61236545-61236552 chr3:61236541-61236554 chr3:61236543-61236552 chr3:61236542-61236553 chr3:61236539-61236554
3	PBX3	chr3:61236951-61237428	A549	lung:	n/a	chr3:61236952-61236972
4	HCFC1	chr3:61235520-61237543	K562	blood:	n/a	n/a
5	YY1	chr3:61236906-61237383	GM12891	blood:	n/a	chr3:61237163-61237171 chr3:61237165-61237173 chr3:61237164-61237174 chr3:61237152-61237174 chr3:61237162-61237174 chr3:61237156-61237176
6	NFYB	chr3:61236936-61237798	GM12878	blood:	n/a	n/a
7	SP1	chr3:61236896-61237482	GM12878	blood:	n/a	chr3:61237226-61237247 chr3:61237150-61237162 chr3:61237147-61237161 chr3:61236962-61236971 chr3:61237152-61237161 chr3:61236963-61236972 chr3:61237150-61237162 chr3:61237150-61237161 chr3:61236961-61236973 chr3:61236962-61236971
8	SP1	chr3:61236848-61237553	A549	lung:	n/a	chr3:61237226-61237247 chr3:61237150-61237162 chr3:61237147-61237161 chr3:61236962-61236971 chr3:61237152-61237161 chr3:61236963-61236972 chr3:61237150-61237162 chr3:61237150-61237161 chr3:61236961-61236973 chr3:61236962-61236971
9	MAFF	chr3:61237070-61237348	HepG2	liver:	n/a	n/a
10	ZNF143	chr3:61236597-61237444	H1-hESC	embryonic stem cell:	n/a	chr3:61236868-61236878 chr3:61237124-61237142
11	ZBTB7A	chr3:61236940-61237315	K562	blood:	n/a	n/a
12	TCF12	chr3:61236681-61237441	ECC-1	luminal epithelium:	n/a	n/a
13	ETS1	chr3:61237062-61237271	A549	lung:	n/a	chr3:61237122-61237135
14	POLR2A	chr3:61236848-61237426	K562	blood:	n/a	n/a
15	E2F6	chr3:61236960-61237348	K562	blood:	n/a	chr3:61237265-61237277 chr3:61237269-61237276 chr3:61237268-61237277 chr3:61237269-61237276 chr3:61237269-61237276
16	YY1	chr3:61236836-61237549	GM12878	blood:	n/a	chr3:61237163-61237171 chr3:61237165-61237173 chr3:61237164-61237174 chr3:61237152-61237174 chr3:61237162-61237174 chr3:61237156-61237176 chr3:61236861-61236875
17	RAD21	chr3:61236943-61237266	H1-hESC	embryonic stem cell:	n/a	n/a
18	ZNF143	chr3:61235406-61237540	GM12878	blood:	n/a	chr3:61235890-61235908 chr3:61236868-61236878 chr3:61235755-61235764 chr3:61235753-61235762 chr3:61237124-61237142 chr3:61235460-61235469 chr3:61235806-61235824 chr3:61235894-61235913 chr3:61235462-61235471
19	MAX	chr3:61236860-61237459	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr3:61235535-61237476	HepG2	liver:	n/a	chr3:61236542-61236553 chr3:61236545-61236552 chr3:61236541-61236554 chr3:61236543-61236552 chr3:61236542-61236553 chr3:61236539-61236554
21	RUNX3	chr3:61236898-61237710	GM12878	blood:	n/a	n/a
22	YY1	chr3:61236908-61237410	HepG2	liver:	n/a	chr3:61237163-61237171 chr3:61237165-61237173 chr3:61237164-61237174 chr3:61237152-61237174 chr3:61237162-61237174 chr3:61237156-61237176
23	SIX5	chr3:61236857-61237369	GM12878	blood:	n/a	n/a
24	YY1	chr3:61236714-61237731	SK-N-SH	brain:	n/a	chr3:61237163-61237171 chr3:61237165-61237173 chr3:61237164-61237174 chr3:61237152-61237174 chr3:61237162-61237174 chr3:61237156-61237176 chr3:61236861-61236875
25	ELF1	chr3:61236911-61237244	K562	blood:	n/a	n/a
26	YY1	chr3:61236890-61237399	SK-N-SH_RA	brain:	n/a	chr3:61237163-61237171 chr3:61237165-61237173 chr3:61237164-61237174 chr3:61237152-61237174 chr3:61237162-61237174 chr3:61237156-61237176
27	POLR2A	chr3:61236534-61237678	H1-hESC	embryonic stem cell:	n/a	n/a
28	USF1	chr3:61236907-61237296	H1-hESC	embryonic stem cell:	n/a	n/a
29	TAF1	chr3:61236889-61237256	K562	blood:	n/a	n/a
30	POLR2A	chr3:61235572-61237455	GM15510	blood:	n/a	n/a
31	YY1	chr3:61236525-61237391	GM12892	blood:	n/a	chr3:61237163-61237171 chr3:61237165-61237173 chr3:61237164-61237174 chr3:61237152-61237174 chr3:61237162-61237174 chr3:61237156-61237176 chr3:61236861-61236875
32	ZC3H11A	chr3:61237104-61237430	K562	blood:	n/a	n/a
33	YY1	chr3:61237038-61237361	HCT-116	colon:	n/a	chr3:61237163-61237171 chr3:61237165-61237173 chr3:61237164-61237174 chr3:61237152-61237174 chr3:61237162-61237174 chr3:61237156-61237176
34	RAD21	chr3:61236919-61237344	HepG2	liver:	n/a	n/a
35	POLR2A	chr3:61236486-61237241	K562	blood:	n/a	n/a
36	POLR2A	chr3:61237163-61237338	H1-hESC	embryonic stem cell:	n/a	n/a
37	MTA3	chr3:61237096-61237791	GM12878	blood:	n/a	n/a
38	MYBL2	chr3:61236868-61237337	HepG2	liver:	n/a	n/a
39	MYC	chr3:61235476-61237686	MCF10A-Er-Src	breast:	n/a	chr3:61236542-61236553 chr3:61236545-61236552 chr3:61236541-61236554 chr3:61236543-61236552 chr3:61236542-61236553 chr3:61236539-61236554
40	POLR2A	chr3:61236514-61237491	GM19193	blood:	n/a	n/a
41	YY1	chr3:61236619-61237486	HepG2	liver:	n/a	chr3:61237163-61237171 chr3:61237165-61237173 chr3:61237164-61237174 chr3:61237152-61237174 chr3:61237162-61237174 chr3:61237156-61237176 chr3:61236861-61236875
42	SP1	chr3:61236881-61237411	HepG2	liver:	n/a	chr3:61237226-61237247 chr3:61237150-61237162 chr3:61237147-61237161 chr3:61236962-61236971 chr3:61237152-61237161 chr3:61236963-61236972 chr3:61237150-61237162 chr3:61237150-61237161 chr3:61236961-61236973 chr3:61236962-61236971
43	POLR2A	chr3:61236383-61237355	GM12892	blood:	n/a	n/a
44	BHLHE40	chr3:61235507-61237676	K562	blood:	n/a	n/a
45	YY1	chr3:61236657-61237376	K562	blood:	n/a	chr3:61237163-61237171 chr3:61237165-61237173 chr3:61237164-61237174 chr3:61237152-61237174 chr3:61237162-61237174 chr3:61237156-61237176 chr3:61236861-61236875
46	SIN3AK20	chr3:61236912-61237299	HepG2	liver:	n/a	n/a
47	ZNF143	chr3:61235411-61237448	K562	blood:	n/a	chr3:61235890-61235908 chr3:61236868-61236878 chr3:61235755-61235764 chr3:61235753-61235762 chr3:61237124-61237142 chr3:61235460-61235469 chr3:61235806-61235824 chr3:61235894-61235913 chr3:61235462-61235471
48	ETS1	chr3:61236931-61237349	GM12878	blood:	n/a	chr3:61237122-61237135
49	STAT1	chr3:61236444-61237501	GM12878	blood:	n/a	chr3:61237131-61237139 chr3:61237366-61237377
50	POLR2A	chr3:61236872-61237394	ECC-1	luminal epithelium:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:61237217-61237267	HCT-116	colon:	n/a
2	chr3:61237217-61237267	IMR90	lung:	fetal
3	chr3:61237206-61237256	HCF	heart:	n/a
4	chr3:61237206-61237256	NH-A	brain:	n/a
5	chr3:61237217-61237267	A549	lung:	n/a
6	chr3:61237217-61237267	BJ	skin:	n/a
7	chr3:61237206-61237256	HIPEpiC	eye:	n/a
8	chr3:61237223-61237273	HIPEpiC	eye:	n/a
9	chr3:61237217-61237267	NT2-D1	testis:	n/a
10	chr3:61237223-61237273	LNCaP	prostate:	n/a
11	chr3:61237206-61237256	MCF-7	breast:	n/a
12	chr3:61237206-61237256	SK-N-SH_RA	brain:	n/a
13	chr3:61237206-61237256	SK-N-SH	brain:	n/a
14	chr3:61237217-61237267	HCM	heart:	n/a
15	chr3:61237206-61237256	RPTEC	kidney:	n/a
16	chr3:61237223-61237273	AoSMC	blood vessel:	n/a
17	chr3:61237217-61237267	GM12891	blood:	n/a
18	chr3:61237223-61237273	Caco-2	colon:	n/a
19	chr3:61237223-61237273	H1-hESC	embryonic stem cell:	embryo
20	chr3:61237223-61237273	Hela-S3	cervix:	n/a
21	chr3:61237206-61237256	PrEC	prostate:	n/a
22	chr3:61237206-61237256	HMEC	breast:	n/a
23	chr3:61237217-61237267	AoSMC	blood vessel:	n/a
24	chr3:61237223-61237273	NHDF-neo	bronchial:	n/a
25	chr3:61237217-61237267	HRCEpiC	kidney:	n/a
26	chr3:61237206-61237256	Jurkat	blood:	n/a
27	chr3:61237223-61237273	AG10803	skin:	n/a
28	chr3:61237206-61237256	Hepatocyte	liver:	n/a
29	chr3:61237223-61237273	HCM	heart:	n/a
30	chr3:61237206-61237256	NHDF-neo	bronchial:	n/a
31	chr3:61237223-61237273	SAEC	small airway:	n/a
32	chr3:61237217-61237267	K562	blood:	n/a
33	chr3:61237206-61237256	H1-hESC	embryonic stem cell:	embryo
34	chr3:61237223-61237273	SKMC	muscle:	n/a
35	chr3:61237217-61237267	Jurkat	blood:	n/a
36	chr3:61237217-61237267	ovcar-3	ovarian:	n/a
37	chr3:61237223-61237273	HPAEpiC	pulmonary alveolar:	n/a
38	chr3:61237223-61237273	HEK293	kidney:	embryo
39	chr3:61237223-61237273	SK-N-SH_RA	brain:	n/a
40	chr3:61237223-61237273	PANC-1	pancreas:	n/a
41	chr3:61237223-61237273	PFSK-1	brain:	n/a
42	chr3:61237206-61237256	HUVEC	blood vessel:	n/a
43	chr3:61237223-61237273	Hepatocyte	liver:	n/a
44	chr3:61237223-61237273	NT2-D1	testis:	n/a
45	chr3:61237223-61237273	GM12891	blood:	n/a
46	chr3:61237223-61237273	AG04450	lung:	fetal
47	chr3:61237206-61237256	MCF10A-Er-Src	breast:	n/a
48	chr3:61237206-61237256	AG10803	skin:	n/a
49	chr3:61237206-61237256	A549	lung:	n/a
50	chr3:61237223-61237273	HRE	kidney:	n/a

Variant related genes	Relation type
FHIT	TF binding region
FHIT	CpG island

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10510864	0.80[ASN][1000 genomes]
rs11707666	0.89[ASN][1000 genomes]
rs11711696	0.89[ASN][1000 genomes]
rs12486043	0.85[ASN][1000 genomes]
rs12488069	0.87[ASN][1000 genomes]
rs12495661	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12497257	0.85[ASN][1000 genomes]
rs12498118	0.87[ASN][1000 genomes]
rs1453741	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17064663	0.85[ASN][1000 genomes]
rs17064715	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1851784	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34371746	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4458366	0.89[ASN][1000 genomes]
rs6799813	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs879365	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9839448	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9839707	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9871848	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876866	chr3:61054494-61310328	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv876867	chr3:61054494-61474575	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1000378	chr3:61103229-61238089	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv876868	chr3:61145050-61282503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv532626	chr3:61159646-61388418	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1008399	chr3:61176965-61461349	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61235400-61237400	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr3:61235400-61237800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr3:61235600-61237800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr3:61235600-61237800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr3:61235600-61237800	Active TSS	Left Ventricle	heart
6	chr3:61235600-61238000	Active TSS	Colonic Mucosa	Colon
7	chr3:61235600-61238000	Active TSS	A549	lung
8	chr3:61235600-61238200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:61235800-61237600	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr3:61235800-61237800	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr3:61235800-61237800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:61235800-61238000	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr3:61235800-61238000	Active TSS	Fetal Brain Female	brain
14	chr3:61235800-61238000	Active TSS	Psoas Muscle	Psoas
15	chr3:61236000-61237800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr3:61236000-61237800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:61236000-61237800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:61236000-61237800	Active TSS	NH-A	brain
19	chr3:61236000-61238000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:61236000-61238200	Active TSS	Aorta	Aorta
21	chr3:61236200-61237600	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr3:61236200-61237600	Active TSS	Muscle Satellite Cultured Cells	--
23	chr3:61236200-61237600	Active TSS	Brain Germinal Matrix	brain
24	chr3:61236200-61237800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr3:61236200-61237800	Active TSS	Brain Substantia Nigra	brain
26	chr3:61236200-61237800	Active TSS	Esophagus	oesophagus
27	chr3:61236200-61237800	Active TSS	Stomach Smooth Muscle	stomach
28	chr3:61236400-61237600	Active TSS	Small Intestine	intestine
29	chr3:61236400-61237800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:61236400-61237800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:61236400-61237800	Active TSS	Colon Smooth Muscle	Colon
32	chr3:61236400-61237800	Active TSS	Fetal Intestine Small	intestine
33	chr3:61236400-61237800	Active TSS	K562	blood
34	chr3:61236400-61237800	Active TSS	NHLF	lung
35	chr3:61236400-61238000	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr3:61236400-61238000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:61236400-61238000	Active TSS	Fetal Intestine Large	intestine
38	chr3:61236400-61238000	Active TSS	Ovary	ovary
39	chr3:61236400-61238000	Active TSS	NHDF-Ad	bronchial
40	chr3:61236400-61238200	Active TSS	Right Atrium	heart
41	chr3:61236600-61237400	Active TSS	Primary T cells from cord blood	blood
42	chr3:61236600-61237400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:61236600-61237400	Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr3:61236600-61237600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr3:61236600-61237600	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr3:61236600-61237600	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr3:61236600-61237600	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr3:61236600-61237600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:61236600-61237600	Active TSS	Rectal Mucosa Donor 31	rectum
50	chr3:61236600-61237600	Active TSS	HepG2	liver

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