Variant report

Variant	rs3745446
Chromosome Location	chr19:56165065-56165066
allele	A/G
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	NFIC	chr19:56165037-56165800	HepG2	liver:	n/a	n/a
2	NFATC1	chr19:56164940-56165801	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:56165031-56167285	ProgFib	skin:	n/a	n/a
4	POLR2A	chr19:56164916-56167231	NB4	blood:	n/a	n/a
5	POLR2A	chr19:56164979-56165809	H1-hESC	embryonic stem cell:	n/a	n/a
6	USF1	chr19:56164946-56166109	A549	lung:	n/a	chr19:56165519-56165535 chr19:56165625-56165641
7	SIN3AK20	chr19:56164921-56165802	A549	lung:	n/a	n/a
8	TCF12	chr19:56164957-56165809	A549	lung:	n/a	n/a
9	POLR2A	chr19:56164945-56167518	K562	blood:	n/a	n/a
10	MAX	chr19:56164887-56166178	K562	blood:	n/a	n/a
11	POLR2A	chr19:56164946-56166106	HUVEC	blood vessel:	n/a	n/a
12	TAF1	chr19:56164951-56165698	H1-hESC	embryonic stem cell:	n/a	n/a
13	EP300	chr19:56164956-56165347	SK-N-SH_RA	brain:	n/a	chr19:56165239-56165255 chr19:56165212-56165219
14	EBF1	chr19:56165029-56166586	GM12878	blood:	n/a	chr19:56165877-56165888 chr19:56165764-56165773
15	CTCF	chr19:56164910-56165679	K562	blood:	n/a	chr19:56165177-56165186 chr19:56165177-56165190 chr19:56165175-56165191 chr19:56165174-56165192 chr19:56165176-56165197
16	NFIC	chr19:56165000-56165398	HepG2	liver:	n/a	n/a
17	BHLHE40	chr19:56164964-56167362	GM12878	blood:	n/a	chr19:56166743-56166759 chr19:56165519-56165535 chr19:56166661-56166670 chr19:56165625-56165641 chr19:56166655-56166676 chr19:56166659-56166672 chr19:56166662-56166671
18	POLR2A	chr19:56164939-56167194	MCF10A-Er-Src	breast:	n/a	n/a
19	SP4	chr19:56164952-56166291	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr19:56164949-56167718	Hela-S3	cervix:	n/a	n/a
21	RAD21	chr19:56165020-56165408	ECC-1	luminal epithelium:	n/a	chr19:56165175-56165194 chr19:56165180-56165192 chr19:56165178-56165191 chr19:56165180-56165190
22	MTA3	chr19:56164959-56165726	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:56164963-56167641	GM12892	blood:	n/a	n/a
24	CEBPB	chr19:56164986-56165385	A549	lung:	n/a	n/a
25	POLR2A	chr19:56164855-56168213	PANC-1	pancreas:	n/a	n/a
26	IRF4	chr19:56165017-56165433	GM12878	blood:	n/a	n/a
27	SIN3AK20	chr19:56164937-56165404	K562	blood:	n/a	n/a
28	EP300	chr19:56165046-56165696	HepG2	liver:	n/a	chr19:56165603-56165617 chr19:56165239-56165255 chr19:56165212-56165219
29	TCF7L2	chr19:56165029-56166037	Hela-S3	cervix:	n/a	n/a
30	HCFC1	chr19:56164938-56168188	Hela-S3	cervix:	n/a	n/a
31	ZMIZ1	chr19:56164969-56166138	K562	blood:	n/a	n/a
32	TBL1XR1	chr19:56164987-56167432	GM12878	blood:	n/a	n/a
33	SP2	chr19:56165036-56165341	HepG2	liver:	n/a	n/a
34	RCOR1	chr19:56165007-56167144	Hela-S3	cervix:	n/a	n/a
35	ELF1	chr19:56164961-56167380	HCT-116	colon:	n/a	chr19:56166912-56166921 chr19:56165209-56165220 chr19:56165210-56165219 chr19:56166458-56166470
36	SRF	chr19:56165038-56165212	HepG2	liver:	n/a	n/a
37	ELF1	chr19:56165022-56166128	SK-N-SH	brain:	n/a	chr19:56165209-56165220 chr19:56165210-56165219
38	POLR2A	chr19:56165009-56165871	HepG2	liver:	n/a	n/a
39	RCOR1	chr19:56164992-56166144	GM12878	blood:	n/a	n/a
40	POLR2A	chr19:56164938-56166286	GM12892	blood:	n/a	n/a
41	CTCF	chr19:56164958-56165363	T-47D	breast:	n/a	chr19:56165177-56165186 chr19:56165177-56165190 chr19:56165175-56165191 chr19:56165174-56165192 chr19:56165176-56165197
42	CTCFL	chr19:56165022-56165301	K562	blood:	n/a	chr19:56165181-56165190
43	RAD21	chr19:56164970-56165374	GM12878	blood:	n/a	chr19:56165175-56165194 chr19:56165180-56165192 chr19:56165178-56165191 chr19:56165180-56165190
44	CTCF	chr19:56164876-56165325	HepG2	liver:	n/a	chr19:56165177-56165186 chr19:56165177-56165190 chr19:56165175-56165191 chr19:56165174-56165192 chr19:56165176-56165197
45	HMGN3	chr19:56164368-56166029	K562	blood:	n/a	n/a
46	GABPA	chr19:56165051-56165282	GM12878	blood:	n/a	chr19:56165241-56165252 chr19:56165243-56165252 chr19:56165241-56165255 chr19:56165238-56165252
47	TCF3	chr19:56164938-56165351	GM12878	blood:	n/a	n/a
48	GABPA	chr19:56165038-56165339	HepG2	liver:	n/a	chr19:56165241-56165252 chr19:56165243-56165252 chr19:56165241-56165255 chr19:56165238-56165252
49	CTCF	chr19:56164991-56165660	MCF-7	breast:	n/a	chr19:56165177-56165186 chr19:56165177-56165190 chr19:56165175-56165191 chr19:56165174-56165192 chr19:56165176-56165197
50	SP2	chr19:56165061-56165316	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:56109380..56112832-chr19:56163189..56166704,4	K562	blood:
2	chr19:56143418..56144411-chr19:56164674..56165216,3	MCF-7	breast:
3	chr19:56164558..56166993-chr20:49346694..49348650,2	MCF-7	breast:
4	chr19:17412304..17413804-chr19:56163545..56165286,2	MCF-7	breast:
5	chr19:55894962..55896497-chr19:56164481..56166264,2	K562	blood:
6	chr19:56110522..56112658-chr19:56163189..56166668,4	K562	blood:
7	chr19:55580785..55582865-chr19:56164262..56165799,2	MCF-7	breast:
8	chr19:55918119..55920865-chr19:56163713..56165863,3	K562	blood:
9	chr19:55591162..55592907-chr19:56164329..56166791,2	K562	blood:
10	chr19:55684227..55686502-chr19:56163659..56165514,2	K562	blood:
11	chr19:56145825..56146505-chr19:56164662..56165252,2	K562	blood:
12	chr19:56164975..56168855-chr19:56176069..56182259,9	MCF-7	breast:
13	chr19:55986503..55989848-chr19:56164025..56167760,5	K562	blood:
14	chr19:56110653..56113509-chr19:56160158..56165183,5	MCF-7	breast:
15	chr19:56165049..56166864-chr19:56826052..56827910,2	K562	blood:
16	chr19:55972391..55974736-chr19:56164397..56167331,2	MCF-7	breast:
17	chr1:154989697..154990248-chr19:56164704..56165234,2	MCF-7	breast:
18	chr19:55897327..55900767-chr19:56164045..56167151,4	K562	blood:
19	chr19:56164666..56171824-chr19:56183341..56192911,16	MCF-7	breast:
20	chr19:55970859..55974182-chr19:56164245..56166880,4	K562	blood:
21	chr19:56134460..56137185-chr19:56162633..56166165,3	K562	blood:
22	chr19:55897327..55899035-chr19:56164311..56166921,2	K562	blood:
23	chr19:55994694..55998007-chr19:56163812..56166427,4	K562	blood:
24	chr19:56028047..56028825-chr19:56164679..56165319,2	K562	blood:
25	chr19:56164264..56167135-chr19:56631802..56633967,4	K562	blood:
26	chr19:54973891..54975551-chr19:56164763..56166635,2	K562	blood:
27	chr19:55894527..55896497-chr19:56163809..56165981,2	K562	blood:
28	chr19:56154378..56155395-chr19:56164636..56165646,5	K562	blood:
29	chr19:56164701..56165323-chr19:56320540..56321426,2	MCF-7	breast:
30	chr19:56164686..56165236-chr19:56205383..56205917,2	MCF-7	breast:
31	chr19:56154666..56155441-chr19:56164653..56165540,4	MCF-7	breast:
32	chr19:56110285..56113089-chr19:56164482..56167654,4	MCF-7	breast:
33	chr19:55579330..55580947-chr19:56164078..56166012,2	MCF-7	breast:
34	chr19:56134221..56137618-chr19:56162633..56168532,10	K562	blood:
35	chr19:56116757..56118714-chr19:56164640..56166848,2	MCF-7	breast:

Variant related genes	Relation type
U2AF2	TF binding region
ENSG00000179922	Chromatin interaction
ENSG00000142409	Chromatin interaction
ENSG00000160439	Chromatin interaction
ENSG00000131848	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000131037	Chromatin interaction
ENSG00000267523	Chromatin interaction
ENSG00000090971	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000267096	Chromatin interaction
ENSG00000182909	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000197483	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000269859	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000063245	Chromatin interaction
ENSG00000130312	Chromatin interaction
ENSG00000267549	Chromatin interaction
ENSG00000179943	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10402618	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10403866	0.84[ASN][1000 genomes]
rs10410802	0.81[ASN][1000 genomes]
rs10415521	0.81[ASN][1000 genomes]
rs10417539	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11882031	0.81[ASN][1000 genomes]
rs2280255	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2287791	0.90[ASN][1000 genomes]
rs28375493	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28385383	0.81[ASN][1000 genomes]
rs28595590	0.81[ASN][1000 genomes]
rs28668166	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs310437	0.83[ASN][1000 genomes]
rs310441	0.88[ASN][1000 genomes]
rs310472	0.86[ASN][1000 genomes]
rs310473	0.84[ASN][1000 genomes]
rs3826757	0.87[ASN][1000 genomes]
rs4801526	0.93[ASN][1000 genomes]
rs523509	0.95[ASN][1000 genomes]
rs575274	0.91[EUR][1000 genomes]
rs57544196	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs584405	0.88[ASN][1000 genomes]
rs58490076	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs610811	0.91[EUR][1000 genomes]
rs617073	0.88[ASN][1000 genomes]
rs648651	0.83[ASN][1000 genomes]
rs681804	0.88[ASN][1000 genomes]
rs73613281	0.84[ASN][1000 genomes]
rs8100143	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
5	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
7	nsv912504	chr19:56149077-56170415	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
8	nsv833882	chr19:56158633-56326564	Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	esv3430993	chr19:56163590-56165588	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56160000-56165200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:56160200-56165200	Weak transcription	Small Intestine	intestine
3	chr19:56160400-56165200	Weak transcription	NHDF-Ad	bronchial
4	chr19:56160800-56165200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr19:56160800-56165200	Weak transcription	Gastric	stomach
6	chr19:56160800-56165200	Weak transcription	Left Ventricle	heart
7	chr19:56160800-56165200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr19:56161000-56165200	Weak transcription	Pancreas	Pancrea
9	chr19:56161000-56165200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr19:56161200-56165200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr19:56161200-56165200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr19:56161200-56165200	Weak transcription	Right Atrium	heart
13	chr19:56161200-56165200	Weak transcription	Stomach Mucosa	stomach
14	chr19:56161800-56165200	Weak transcription	Lung	lung
15	chr19:56162200-56165200	Weak transcription	Ovary	ovary
16	chr19:56163400-56167800	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr19:56163400-56168000	Active TSS	H9 Cell Line	embryonic stem cell
18	chr19:56163400-56168200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr19:56163600-56167800	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr19:56163600-56167800	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr19:56163600-56168000	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr19:56164000-56165200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:56164000-56165200	Weak transcription	Spleen	Spleen
24	chr19:56164000-56165200	Weak transcription	GM12878-XiMat	blood
25	chr19:56164200-56165200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:56164200-56168000	Active TSS	H1 Cell Line	embryonic stem cell
27	chr19:56164400-56165200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr19:56164400-56165200	Enhancers	Fetal Brain Male	brain
29	chr19:56164400-56166400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr19:56164400-56167000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr19:56164400-56167200	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr19:56164400-56167200	Active TSS	NHEK	skin
33	chr19:56164400-56167600	Active TSS	Hela-S3	cervix
34	chr19:56164400-56167800	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr19:56164400-56168000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr19:56164400-56168000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr19:56164400-56168400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr19:56164600-56165200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr19:56164600-56167000	Active TSS	Rectal Smooth Muscle	rectum
40	chr19:56164600-56167200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:56164600-56167200	Active TSS	Colon Smooth Muscle	Colon
42	chr19:56164600-56167200	Active TSS	Osteobl	bone
43	chr19:56164600-56167400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:56164600-56167400	Active TSS	Fetal Brain Female	brain
45	chr19:56164600-56167600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr19:56164600-56167600	Active TSS	Psoas Muscle	Psoas
47	chr19:56164600-56167800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr19:56164600-56167800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr19:56164800-56165200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:56164800-56165200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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