Variant report

Variant	rs562402446
Chromosome Location	chr3:156878937-156878938
allele	-/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:179)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:179 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:156876714-156879143	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr3:156875169-156879293	MCF10A-Er-Src	breast:	n/a	n/a
3	TCF12	chr3:156876865-156878956	A549	lung:	n/a	n/a
4	POLR2A	chr3:156876034-156879187	GM12892	blood:	n/a	n/a
5	STAT3	chr3:156877802-156879280	Hela-S3	cervix:	n/a	n/a
6	TBP	chr3:156877008-156879123	H1-hESC	embryonic stem cell:	n/a	chr3:156878569-156878580
7	MTA3	chr3:156876897-156879216	GM12878	blood:	n/a	n/a
8	GATA2	chr3:156878422-156879137	HUVEC	blood vessel:	n/a	chr3:156878771-156878781 chr3:156878865-156878875
9	POLR2A	chr3:156877099-156878944	GM18526	blood:	n/a	n/a
10	GATA3	chr3:156878305-156879064	T-47D	breast:	n/a	chr3:156878771-156878781 chr3:156878865-156878875
11	POLR2A	chr3:156877455-156879114	HUVEC	blood vessel:	n/a	n/a
12	NFIC	chr3:156877665-156879016	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:156876806-156878978	GM12891	blood:	n/a	n/a
14	POLR2A	chr3:156876253-156879191	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:156876812-156879195	GM12892	blood:	n/a	n/a
16	POLR2A	chr3:156875365-156879216	IMR90	lung:	n/a	n/a
17	POLR2A	chr3:156875302-156879130	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr3:156874371-156879129	GM12891	blood:	n/a	n/a
19	POLR2A	chr3:156876914-156878985	U87	brain:	n/a	n/a
20	POLR2A	chr3:156873921-156879347	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr3:156877656-156879118	K562	blood:	n/a	n/a
22	GTF2F1	chr3:156877745-156879136	Hela-S3	cervix:	n/a	chr3:156878569-156878580
23	POLR2A	chr3:156874146-156879345	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:156876874-156879077	HCT-116	colon:	n/a	n/a
25	EP300	chr3:156877127-156878938	ECC-1	luminal epithelium:	n/a	chr3:156877371-156877380 chr3:156877321-156877330 chr3:156877368-156877377
26	MYC	chr3:156877677-156878942	K562	blood:	n/a	chr3:156877996-156878005
27	POLR2A	chr3:156876946-156879009	Raji	blood:	n/a	n/a
28	TAF1	chr3:156877014-156878956	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr3:156875610-156878980	GM12892	blood:	n/a	n/a
30	RELA	chr3:156877067-156879276	GM18951	blood:	n/a	n/a
31	POLR2A	chr3:156876780-156879065	PANC-1	pancreas:	n/a	n/a
32	POLR2A	chr3:156876874-156878991	U87	brain:	n/a	n/a
33	JUN	chr3:156877416-156879209	K562	blood:	n/a	chr3:156878014-156878023 chr3:156878630-156878642 chr3:156878013-156878026
34	MTA3	chr3:156877535-156879134	GM12878	blood:	n/a	n/a
35	NR2F2	chr3:156877000-156879008	MCF-7	breast:	n/a	n/a
36	RELA	chr3:156877675-156879128	GM18505	blood:	n/a	n/a
37	POLR2A	chr3:156876730-156879055	HepG2	liver:	n/a	n/a
38	RELA	chr3:156876991-156879191	GM12891	blood:	n/a	n/a
39	CEBPB	chr3:156877773-156878970	MCF-7	breast:	n/a	n/a
40	CEBPB	chr3:156877835-156879060	K562	blood:	n/a	n/a
41	TEAD4	chr3:156877486-156879171	K562	blood:	n/a	n/a
42	MYC	chr3:156877124-156878996	K562	blood:	n/a	chr3:156877996-156878005
43	FOXM1	chr3:156877647-156878999	GM12878	blood:	n/a	n/a
44	ZKSCAN1	chr3:156877642-156879097	Hela-S3	cervix:	n/a	n/a
45	BRCA1	chr3:156877774-156879253	Hela-S3	cervix:	n/a	n/a
46	MXI1	chr3:156877050-156879012	Hela-S3	cervix:	n/a	n/a
47	SIN3AK20	chr3:156876741-156879214	MCF-7	breast:	n/a	n/a
48	RCOR1	chr3:156877678-156878976	K562	blood:	n/a	n/a
49	POLR2A	chr3:156875623-156879028	HepG2	liver:	n/a	n/a
50	KAT2A	chr3:156877675-156878944	Hela-S3	cervix:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:156799577..156801238-chr3:156877640..156879746,2	K562	blood:
2	chr3:156270417..156272669-chr3:156876892..156879496,3	MCF-7	breast:
3	chr12:52445120..52446136-chr3:156877833..156878965,3	Hela-S3	cervix:
4	chr15:41624471..41625190-chr3:156878541..156879113,2	Hela-S3	cervix:
5	chr11:65266062..65267005-chr3:156878215..156879104,2	Hela-S3	cervix:
6	chr3:156878407..156879008-chr7:102715174..102716014,2	Hela-S3	cervix:
7	chr3:156533151..156536166-chr3:156876536..156878958,4	MCF-7	breast:
8	chr3:156390967..156393612-chr3:156877452..156879722,5	K562	blood:
9	chr12:49658449..49659329-chr3:156878118..156878938,3	Hela-S3	cervix:
10	chr3:156533566..156537799-chr3:156875553..156879495,5	MCF-7	breast:
11	chr17:61850669..61851474-chr3:156878244..156879352,3	Hela-S3	cervix:
12	chr3:156391251..156395598-chr3:156875832..156879722,8	K562	blood:
13	chr3:156542707..156546513-chr3:156875626..156880471,4	K562	blood:
14	chr1:235530311..235530993-chr3:156878689..156879352,2	Hela-S3	cervix:
15	chr1:245027282..245027917-chr3:156878222..156878967,2	Hela-S3	cervix:
16	chr2:131594435..131595031-chr3:156878104..156879008,2	Hela-S3	cervix:
17	chr3:156390449..156395705-chr3:156876136..156879645,10	MCF-7	breast:
18	chr3:156877990..156879497-chr6:26155874..26158713,2	MCF-7	breast:
19	chr1:169454840..169455424-chr3:156878085..156879028,2	Hela-S3	cervix:
20	chr3:156876658..156879378-chr3:156891661..156893506,34	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000241770	TF binding region
CCNL1	TF binding region
ENSG00000233221	Chromatin interaction
ENSG00000136002	Chromatin interaction
ENSG00000198231	Chromatin interaction
ENSG00000240875	Chromatin interaction
ENSG00000117479	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000153187	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000108588	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000161040	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000116957	Chromatin interaction
ENSG00000213062	Chromatin interaction
ENSG00000137804	Chromatin interaction
ENSG00000123358	Chromatin interaction
ENSG00000197980	Chromatin interaction
ENSG00000222675	Chromatin interaction
ENSG00000114850	Chromatin interaction
ENSG00000104147	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000243176	Chromatin interaction
ENSG00000241544	Chromatin interaction
ENSG00000170632	Chromatin interaction
ENSG00000243926	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

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	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv520331	chr3:156858300-156915650	Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
3	nsv965226	chr3:156878848-156881756	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156871800-156879200	Active TSS	Right Ventricle	heart
2	chr3:156872200-156879000	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
3	chr3:156872400-156879200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:156874800-156879000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:156875000-156879000	Active TSS	Psoas Muscle	Psoas
6	chr3:156875800-156879000	Active TSS	Left Ventricle	heart
7	chr3:156876200-156879000	Active TSS	Small Intestine	intestine
8	chr3:156876400-156879000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:156876600-156879000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr3:156876600-156879000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:156876600-156879000	Active TSS	Fetal Brain Male	brain
12	chr3:156876600-156879200	Active TSS	Fetal Muscle Trunk	muscle
13	chr3:156876800-156879000	Active TSS	H9 Cell Line	embryonic stem cell
14	chr3:156876800-156879200	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr3:156877000-156879000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:156877000-156879000	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr3:156877000-156879000	Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr3:156877000-156879000	Active TSS	Liver	Liver
19	chr3:156877000-156879000	Active TSS	Esophagus	oesophagus
20	chr3:156877000-156879000	Active TSS	Pancreas	Pancrea
21	chr3:156877000-156879000	Active TSS	HSMMtube	muscle
22	chr3:156877000-156879200	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr3:156877000-156879400	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr3:156877000-156879600	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr3:156877200-156879200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:156877800-156879200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:156878000-156879200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:156878000-156879200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:156878200-156879000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:156878200-156879000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:156878200-156879000	Active TSS	Aorta	Aorta
32	chr3:156878200-156879200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
33	chr3:156878200-156879200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr3:156878200-156879200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:156878200-156879200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr3:156878200-156879200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr3:156878200-156879200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:156878200-156879200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:156878200-156879200	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr3:156878200-156879200	Flanking Active TSS	Placenta	Placenta
41	chr3:156878200-156879200	Flanking Active TSS	HUVEC	blood vessel
42	chr3:156878200-156879200	Flanking Active TSS	NH-A	brain
43	chr3:156878200-156879400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:156878200-156879400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:156878400-156879000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:156878400-156879200	Active TSS	Right Atrium	heart
47	chr3:156878600-156879000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:156878600-156879000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:156878600-156879000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:156878600-156879000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links