Variant report

Variant	rs546828028
Chromosome Location	chr3:141205773-141205774
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	MXI1	chr3:141205521-141207007	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:141204645-141205785	U87	brain:	n/a	n/a
3	HMGN3	chr3:141205705-141206833	K562	blood:	n/a	n/a
4	POLR2A	chr3:141205438-141206899	H1-neurons	neurons:	n/a	n/a
5	MAX	chr3:141205692-141206996	NB4	blood:	n/a	chr3:141206243-141206252
6	YY1	chr3:141205743-141206249	K562	blood:	n/a	chr3:141205915-141205935 chr3:141206090-141206104 chr3:141206218-141206227 chr3:141206136-141206145 chr3:141206113-141206122 chr3:141206066-141206077
7	MXI1	chr3:141204940-141207413	IMR90	lung:	n/a	chr3:141204946-141204961
8	PML	chr3:141205761-141206165	K562	blood:	n/a	n/a
9	POLR2A	chr3:141205513-141206933	Raji	blood:	n/a	n/a
10	POLR2A	chr3:141204567-141206988	HepG2	liver:	n/a	n/a
11	GATA3	chr3:141205504-141205850	T-47D	breast:	n/a	n/a
12	POLR2A	chr3:141205731-141207009	GM12878	blood:	n/a	n/a
13	BHLHE40	chr3:141205733-141206940	K562	blood:	n/a	chr3:141206446-141206462 chr3:141206249-141206265
14	YY1	chr3:141205550-141206293	SK-N-SH	brain:	n/a	chr3:141205915-141205935 chr3:141206090-141206104 chr3:141206218-141206227 chr3:141206136-141206145 chr3:141206113-141206122 chr3:141206066-141206077
15	MAZ	chr3:141204422-141207328	IMR90	lung:	n/a	chr3:141204946-141204955 chr3:141205187-141205197 chr3:141206243-141206252
16	EGR1	chr3:141205610-141205936	GM12878	blood:	n/a	chr3:141205764-141205778
17	CTBP2	chr3:141205522-141206871	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr3:141205362-141207319	Hela-S3	cervix:	n/a	n/a
19	REST	chr3:141205209-141207288	H1-neurons	neurons:	n/a	chr3:141206093-141206113
20	POLR2A	chr3:141205391-141206952	HUVEC	blood vessel:	n/a	n/a
21	YY1	chr3:141205689-141206191	SK-N-SH_RA	brain:	n/a	chr3:141205915-141205935 chr3:141206090-141206104 chr3:141206136-141206145 chr3:141206113-141206122 chr3:141206066-141206077
22	POLR2A	chr3:141205235-141206808	IMR90	lung:	n/a	n/a
23	POLR2A	chr3:141204583-141206968	HUVEC	blood vessel:	n/a	n/a
24	MAX	chr3:141205474-141207037	MCF-7	breast:	n/a	chr3:141206243-141206252
25	POLR2A	chr3:141205771-141206189	GM12891	blood:	n/a	n/a
26	YY1	chr3:141205743-141207003	GM12878	blood:	n/a	chr3:141205915-141205935 chr3:141206090-141206104 chr3:141206447-141206461 chr3:141206445-141206456 chr3:141206218-141206227 chr3:141206454-141206465 chr3:141206136-141206145 chr3:141206310-141206324 chr3:141206113-141206122 chr3:141206066-141206077
27	TCF12	chr3:141205370-141207011	ECC-1	luminal epithelium:	n/a	n/a
28	ZKSCAN1	chr3:141205563-141205990	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr3:141205483-141206766	HepG2	liver:	n/a	n/a
30	IRF1	chr3:141205549-141206110	K562	blood:	n/a	n/a
31	POLR2A	chr3:141205528-141206990	K562	blood:	n/a	n/a
32	TAF1	chr3:141205738-141206835	HepG2	liver:	n/a	n/a
33	POLR2A	chr3:141205731-141206924	GM18505	blood:	n/a	n/a
34	POLR2A	chr3:141205732-141206898	GM12892	blood:	n/a	n/a
35	POLR2A	chr3:141205586-141206878	MCF-7	breast:	n/a	n/a
36	YY1	chr3:141205690-141206296	ECC-1	luminal epithelium:	n/a	chr3:141205915-141205935 chr3:141206090-141206104 chr3:141206218-141206227 chr3:141206136-141206145 chr3:141206113-141206122 chr3:141206066-141206077
37	UBTF	chr3:141205707-141206942	K562	blood:	n/a	n/a
38	POLR2A	chr3:141205528-141206999	NB4	blood:	n/a	n/a
39	POLR2A	chr3:141205566-141206110	GM12878	blood:	n/a	n/a
40	MAX	chr3:141205667-141207018	HepG2	liver:	n/a	chr3:141206243-141206252
41	ELF1	chr3:141205766-141206201	GM12878	blood:	n/a	chr3:141206131-141206143
42	MAX	chr3:141205726-141207035	A549	lung:	n/a	chr3:141206243-141206252
43	MYC	chr3:141205573-141206939	K562	blood:	n/a	chr3:141206243-141206252
44	MYC	chr3:141205702-141206852	MCF-7	breast:	n/a	chr3:141206243-141206252
45	EGR1	chr3:141205260-141206676	K562	blood:	n/a	chr3:141205358-141205380 chr3:141206268-141206282 chr3:141206111-141206121 chr3:141206108-141206121 chr3:141205764-141205778 chr3:141206107-141206122 chr3:141206108-141206121
46	POLR2A	chr3:141205613-141206999	GM12892	blood:	n/a	n/a
47	TCF12	chr3:141204664-141206919	A549	lung:	n/a	n/a
48	POLR2A	chr3:141205773-141206925	GM12878	blood:	n/a	n/a
49	MAZ	chr3:141205544-141207059	GM12878	blood:	n/a	chr3:141206243-141206252
50	ZNF263	chr3:141205093-141206085	HEK293-T-REx	kidney:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:141205767-141205817	SKMC	muscle:	n/a
2	chr3:141205767-141205817	AG10803	skin:	n/a
3	chr3:141205767-141205817	HRCEpiC	kidney:	n/a
4	chr3:141205758-141205808	ECC-1	luminal epithelium:	n/a
5	chr3:141205758-141205808	NHDF-neo	bronchial:	n/a
6	chr3:141205767-141205817	HIPEpiC	eye:	n/a
7	chr3:141205767-141205817	NB4	blood:	n/a
8	chr3:141205767-141205817	K562	blood:	n/a
9	chr3:141205758-141205808	SK-N-MC	brain:	n/a
10	chr3:141205767-141205817	HCT-116	colon:	n/a
11	chr3:141205758-141205808	AG10803	skin:	n/a
12	chr3:141205767-141205817	GM19239	blood:	n/a
13	chr3:141205758-141205808	HAEpiC	amniotic membrane:	n/a
14	chr3:141205767-141205817	HCPEpiC	choroid plexus:	n/a
15	chr3:141205758-141205808	LNCaP	prostate:	n/a
16	chr3:141205767-141205817	HCM	heart:	n/a
17	chr3:141205758-141205808	T-47D	breast:	n/a
18	chr3:141205758-141205808	PrEC	prostate:	n/a
19	chr3:141205758-141205808	HCM	heart:	n/a
20	chr3:141205767-141205817	PFSK-1	brain:	n/a
21	chr3:141205758-141205808	NT2-D1	testis:	n/a
22	chr3:141205758-141205808	HCF	heart:	n/a
23	chr3:141205758-141205808	AG09319	gingival:	n/a
24	chr3:141205767-141205817	SK-N-SH_RA	brain:	n/a
25	chr3:141205767-141205817	ovcar-3	ovarian:	n/a
26	chr3:141205758-141205808	HPAEpiC	pulmonary alveolar:	n/a
27	chr3:141205758-141205808	SK-N-SH_RA	brain:	n/a
28	chr3:141205758-141205808	SKMC	muscle:	n/a
29	chr3:141205767-141205817	AG09309	skin:	n/a
30	chr3:141205767-141205817	SK-N-MC	brain:	n/a
31	chr3:141205758-141205808	HCT-116	colon:	n/a
32	chr3:141205767-141205817	SAEC	small airway:	n/a
33	chr3:141205767-141205817	Jurkat	blood:	n/a
34	chr3:141205758-141205808	NB4	blood:	n/a
35	chr3:141205758-141205808	ProgFib	skin:	n/a
36	chr3:141205758-141205808	PFSK-1	brain:	n/a
37	chr3:141205767-141205817	AG04450	lung:	fetal
38	chr3:141205767-141205817	AoSMC	blood vessel:	n/a
39	chr3:141205767-141205817	Caco-2	colon:	n/a
40	chr3:141205758-141205808	A549	lung:	n/a
41	chr3:141205767-141205817	AG09319	gingival:	n/a
42	chr3:141205758-141205808	HEK293	kidney:	embryo
43	chr3:141205758-141205808	GM12891	blood:	n/a
44	chr3:141205767-141205817	PrEC	prostate:	n/a
45	chr3:141205767-141205817	HUVEC	blood vessel:	n/a
46	chr3:141205767-141205817	ECC-1	luminal epithelium:	n/a
47	chr3:141205767-141205817	BJ	skin:	n/a
48	chr3:141205767-141205817	HRPEpiC	eye:	n/a
49	chr3:141205767-141205817	U87	brain:	n/a
50	chr3:141205758-141205808	AG09309	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:141204551..141207938-chr3:141241119..141245308,6	MCF-7	breast:
2	chr3:141189849..141195094-chr3:141204829..141208801,7	MCF-7	breast:
3	chr18:12883912..12884619-chr3:141205723..141206246,2	Hela-S3	cervix:
4	chr3:141085187..141087816-chr3:141204878..141206678,4	MCF-7	breast:
5	chr12:120729229..120730031-chr3:141205706..141206699,3	Hela-S3	cervix:
6	chr3:141205080..141206779-chr6:76458156..76460847,2	MCF-7	breast:
7	chr3:141085737..141089975-chr3:141204779..141207356,5	K562	blood:

Variant related genes	Relation type
RASA2	TF binding region
RASA2	CpG island
ENSG00000177311	Chromatin interaction
ENSG00000175354	Chromatin interaction
ENSG00000250170	Chromatin interaction
ENSG00000249417	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000215606	Chromatin interaction
ENSG00000196586	Chromatin interaction

Extended variants
information (count: 1 )
Associated
traits (count: 0)

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3423260	chr3:141204887-141207435	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141204200-141205800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr3:141204200-141208000	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr3:141204400-141205800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr3:141204600-141205800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:141204600-141205800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:141204800-141205800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr3:141204800-141207400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr3:141205000-141207000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:141205000-141207000	Active TSS	Fetal Kidney	kidney
10	chr3:141205000-141207400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr3:141205000-141207600	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr3:141205200-141205800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
13	chr3:141205200-141205800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:141205200-141205800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:141205200-141205800	Active TSS	Right Atrium	heart
16	chr3:141205200-141205800	Flanking Active TSS	Dnd41	blood
17	chr3:141205200-141206000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:141205200-141206200	Active TSS	Brain Germinal Matrix	brain
19	chr3:141205200-141207000	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr3:141205200-141207000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:141205200-141207000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:141205200-141207000	Active TSS	Fetal Brain Female	brain
23	chr3:141205200-141207200	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr3:141205200-141207200	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr3:141205200-141207200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:141205200-141207200	Active TSS	Brain Substantia Nigra	brain
27	chr3:141205200-141207400	Active TSS	H1 Cell Line	embryonic stem cell
28	chr3:141205200-141207400	Active TSS	Brain Cingulate Gyrus	brain
29	chr3:141205400-141205800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
30	chr3:141205400-141205800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:141205400-141205800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:141205400-141205800	Flanking Active TSS	Fetal Muscle Leg	muscle
33	chr3:141205400-141205800	Flanking Active TSS	Placenta	Placenta
34	chr3:141205400-141205800	Flanking Active TSS	Fetal Thymus	thymus
35	chr3:141205400-141205800	Weak transcription	Spleen	Spleen
36	chr3:141205400-141206800	Active TSS	Brain Hippocampus Middle	brain
37	chr3:141205400-141206800	Active TSS	Stomach Smooth Muscle	stomach
38	chr3:141205400-141207000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:141205400-141207000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:141205400-141207000	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr3:141205400-141207000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:141205400-141207000	Active TSS	Aorta	Aorta
43	chr3:141205400-141207000	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr3:141205400-141207000	Active TSS	Esophagus	oesophagus
45	chr3:141205400-141207000	Active TSS	Gastric	stomach
46	chr3:141205400-141207000	Active TSS	Left Ventricle	heart
47	chr3:141205400-141207000	Active TSS	Ovary	ovary
48	chr3:141205400-141207000	Active TSS	Pancreas	Pancrea
49	chr3:141205400-141207000	Active TSS	Placenta Amnion	Placenta Amnion
50	chr3:141205400-141207000	Active TSS	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links