Variant report

Variant	rs2280255
Chromosome Location	chr19:56165921-56165922
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	chr19:56165031-56167285	ProgFib	skin:	n/a	n/a
2	POLR2A	chr19:56164916-56167231	NB4	blood:	n/a	n/a
3	USF1	chr19:56164946-56166109	A549	lung:	n/a	chr19:56165519-56165535 chr19:56165625-56165641
4	POLR2A	chr19:56164945-56167518	K562	blood:	n/a	n/a
5	MAX	chr19:56164887-56166178	K562	blood:	n/a	n/a
6	POLR2A	chr19:56164946-56166106	HUVEC	blood vessel:	n/a	n/a
7	EBF1	chr19:56165029-56166586	GM12878	blood:	n/a	chr19:56165877-56165888 chr19:56165764-56165773
8	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
9	POLR2A	chr19:56164939-56167194	MCF10A-Er-Src	breast:	n/a	n/a
10	SP4	chr19:56164952-56166291	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr19:56164949-56167718	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr19:56164963-56167641	GM12892	blood:	n/a	n/a
13	HNF4G	chr19:56165531-56166781	HepG2	liver:	n/a	n/a
14	POLR2A	chr19:56164855-56168213	PANC-1	pancreas:	n/a	n/a
15	TCF7L2	chr19:56165029-56166037	Hela-S3	cervix:	n/a	n/a
16	HCFC1	chr19:56164938-56168188	Hela-S3	cervix:	n/a	n/a
17	ZMIZ1	chr19:56164969-56166138	K562	blood:	n/a	n/a
18	TBL1XR1	chr19:56164987-56167432	GM12878	blood:	n/a	n/a
19	RCOR1	chr19:56165007-56167144	Hela-S3	cervix:	n/a	n/a
20	ELF1	chr19:56164961-56167380	HCT-116	colon:	n/a	chr19:56166912-56166921 chr19:56165209-56165220 chr19:56165210-56165219 chr19:56166458-56166470
21	ELF1	chr19:56165022-56166128	SK-N-SH	brain:	n/a	chr19:56165209-56165220 chr19:56165210-56165219
22	RCOR1	chr19:56164992-56166144	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:56164938-56166286	GM12892	blood:	n/a	n/a
24	HMGN3	chr19:56164368-56166029	K562	blood:	n/a	n/a
25	POLR2A	chr19:56164905-56167273	K562	blood:	n/a	n/a
26	POLR2A	chr19:56164961-56166170	GM12891	blood:	n/a	n/a
27	MAZ	chr19:56164940-56167582	IMR90	lung:	n/a	chr19:56166757-56166772 chr19:56167157-56167173 chr19:56166761-56166771 chr19:56166756-56166775 chr19:56166759-56166774 chr19:56166762-56166771 chr19:56166759-56166768 chr19:56166760-56166770 chr19:56166761-56166770
28	POLR2A	chr19:56164986-56167431	HL-60	blood:	n/a	n/a
29	ATF2	chr19:56165005-56166235	GM12878	blood:	n/a	n/a
30	MAX	chr19:56164967-56167360	Hela-S3	cervix:	n/a	chr19:56166757-56166772 chr19:56167157-56167173 chr19:56166761-56166771 chr19:56166756-56166775 chr19:56166759-56166774 chr19:56166762-56166771 chr19:56166759-56166768 chr19:56166760-56166770 chr19:56166761-56166770
31	ELK1	chr19:56164985-56167377	Hela-S3	cervix:	n/a	chr19:56166917-56166926 chr19:56166917-56166926
32	ETS1	chr19:56164931-56167444	A549	lung:	n/a	chr19:56166917-56166926 chr19:56165721-56165730 chr19:56165211-56165220 chr19:56165211-56165220 chr19:56166917-56166926 chr19:56166909-56166919 chr19:56166917-56166926 chr19:56165166-56165173 chr19:56166916-56166929 chr19:56166915-56166925 chr19:56166917-56166926 chr19:56166909-56166920 chr19:56166917-56166926 chr19:56166917-56166926 chr19:56166915-56166926 chr19:56166911-56166920 chr19:56166908-56166923 chr19:56165163-56165176 chr19:56165351-56165360 chr19:56166914-56166930
33	SP1	chr19:56164828-56167246	A549	lung:	n/a	chr19:56166945-56166955 chr19:56167017-56167031 chr19:56166996-56167003
34	RELA	chr19:56165021-56166198	GM19099	blood:	n/a	n/a
35	POLR2A	chr19:56164973-56167415	IMR90	lung:	n/a	n/a
36	MAX	chr19:56164947-56167599	HCT-116	colon:	n/a	chr19:56166757-56166772 chr19:56167157-56167173 chr19:56166761-56166771 chr19:56166756-56166775 chr19:56166759-56166774 chr19:56166762-56166771 chr19:56166759-56166768 chr19:56166760-56166770 chr19:56166761-56166770
37	GABPA	chr19:56164927-56167232	K562	blood:	n/a	chr19:56165241-56165252 chr19:56165357-56165368 chr19:56166731-56166745 chr19:56165441-56165452 chr19:56166731-56166742 chr19:56165243-56165252 chr19:56165484-56165498 chr19:56166684-56166693 chr19:56165438-56165452 chr19:56165241-56165255 chr19:56165357-56165366 chr19:56165357-56165371 chr19:56165487-56165501 chr19:56165487-56165498 chr19:56166733-56166742 chr19:56166914-56166921 chr19:56165354-56165368 chr19:56165487-56165496 chr19:56165441-56165455 chr19:56165238-56165252
38	MBD4	chr19:56165868-56166264	HepG2	liver:	n/a	n/a
39	POLR2A	chr19:56164958-56167379	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr19:56165038-56166251	A549	lung:	n/a	n/a
41	MXI1	chr19:56164941-56167520	IMR90	lung:	n/a	chr19:56165279-56165294 chr19:56166760-56166769 chr19:56165281-56165296 chr19:56166762-56166771
42	SIN3A	chr19:56164967-56166122	H1-hESC	embryonic stem cell:	n/a	chr19:56165464-56165475
43	STAT3	chr19:56165542-56166119	MCF10A-Er-Src	breast:	n/a	chr19:56165607-56165618
44	EP300	chr19:56164995-56166158	K562	blood:	n/a	chr19:56165603-56165617 chr19:56165691-56165705 chr19:56165239-56165255 chr19:56165212-56165219
45	POLR2A	chr19:56165030-56165955	H1-neurons	neurons:	n/a	n/a
46	POLR2A	chr19:56165032-56166841	A549	lung:	n/a	n/a
47	MAFK	chr19:56165886-56166155	HepG2	liver:	n/a	n/a
48	POLR2A	chr19:56165007-56166272	GM12878	blood:	n/a	n/a
49	GABPA	chr19:56164952-56167439	SK-N-SH	brain:	n/a	chr19:56165241-56165252 chr19:56165357-56165368 chr19:56166731-56166745 chr19:56165441-56165452 chr19:56166731-56166742 chr19:56165243-56165252 chr19:56165484-56165498 chr19:56166684-56166693 chr19:56165438-56165452 chr19:56165241-56165255 chr19:56165357-56165366 chr19:56165357-56165371 chr19:56165487-56165501 chr19:56165487-56165498 chr19:56166733-56166742 chr19:56166914-56166921 chr19:56165354-56165368 chr19:56165487-56165496 chr19:56165441-56165455 chr19:56165238-56165252
50	USF2	chr19:56165081-56166179	GM12878	blood:	n/a	chr19:56165519-56165535 chr19:56165625-56165641

No.	Distal block	Cell Line	Cell type
1	chr19:56109380..56112832-chr19:56163189..56166704,4	K562	blood:
2	chr19:56165266..56165936-chr2:85555060..85555563,2	Hela-S3	cervix:
3	chr19:56164558..56166993-chr20:49346694..49348650,2	MCF-7	breast:
4	chr19:55894962..55896497-chr19:56164481..56166264,2	K562	blood:
5	chr19:56110522..56112658-chr19:56163189..56166668,4	K562	blood:
6	chr12:54674459..54674991-chr19:56165715..56166335,2	Hela-S3	cervix:
7	chr19:55791629..55793260-chr19:56165234..56166753,2	K562	blood:
8	chr19:55591162..55592907-chr19:56164329..56166791,2	K562	blood:
9	chr19:56164975..56168855-chr19:56176069..56182259,9	MCF-7	breast:
10	chr19:55986503..55989848-chr19:56164025..56167760,5	K562	blood:
11	chr19:55864307..55867114-chr19:56165229..56167152,3	K562	blood:
12	chr19:56165204..56168088-chr19:56651419..56654921,3	MCF-7	breast:
13	chr19:56165463..56168899-chr19:56631045..56633379,3	K562	blood:
14	chr19:56165049..56166864-chr19:56826052..56827910,2	K562	blood:
15	chr19:55972391..55974736-chr19:56164397..56167331,2	MCF-7	breast:
16	chr19:56109729..56112451-chr19:56165377..56168122,5	MCF-7	breast:
17	chr19:55897327..55900767-chr19:56164045..56167151,4	K562	blood:
18	chr19:56164666..56171824-chr19:56183341..56192911,16	MCF-7	breast:
19	chr19:55970859..55974182-chr19:56164245..56166880,4	K562	blood:
20	chr19:56134460..56137185-chr19:56162633..56166165,3	K562	blood:
21	chr19:56115993..56118637-chr19:56165089..56166891,2	K562	blood:
22	chr19:55897327..55899035-chr19:56164311..56166921,2	K562	blood:
23	chr19:55994694..55998007-chr19:56163812..56166427,4	K562	blood:
24	chr19:56165703..56169980-chr19:56194386..56196896,5	MCF-7	breast:
25	chr19:56164264..56167135-chr19:56631802..56633967,4	K562	blood:
26	chr17:62223284..62223856-chr19:56165357..56165947,2	MCF-7	breast:
27	chr19:54973891..54975551-chr19:56164763..56166635,2	K562	blood:
28	chr19:55894527..55896497-chr19:56163809..56165981,2	K562	blood:
29	chr19:56134733..56137004-chr19:56165358..56168098,3	MCF-7	breast:
30	chr19:56165194..56167874-chr19:56829304..56831856,2	K562	blood:
31	chr19:56110285..56113089-chr19:56164482..56167654,4	MCF-7	breast:
32	chr19:55579330..55580947-chr19:56164078..56166012,2	MCF-7	breast:
33	chr19:56134221..56137618-chr19:56162633..56168532,10	K562	blood:
34	chr19:56116757..56118714-chr19:56164640..56166848,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC106-1	chr19:56165498-56166385	NONHSAT068057

Variant related genes	Relation type
U2AF2	TF binding region
ENSG00000160439	Chromatin interaction
ENSG00000267523	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000182909	Chromatin interaction
ENSG00000131848	Chromatin interaction
ENSG00000090971	Chromatin interaction
ENSG00000142409	Chromatin interaction
ENSG00000197483	Chromatin interaction
ENSG00000213014	Chromatin interaction
ENSG00000160471	Chromatin interaction
ENSG00000269859	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000199753	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000267549	Chromatin interaction
ENSG00000267096	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000131037	Chromatin interaction
ENSG00000266402	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000152291	Chromatin interaction
ENSG00000211571	Chromatin interaction
ENSG00000063245	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000133265	Chromatin interaction
ENSG00000135486	Chromatin interaction
ENSG00000167685	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10402618	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10403866	0.82[ASN][1000 genomes]
rs10417539	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2287791	0.89[ASN][1000 genomes]
rs28375493	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28668166	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs310437	0.81[ASN][1000 genomes]
rs310441	0.87[ASN][1000 genomes]
rs310472	0.84[ASN][1000 genomes]
rs310473	0.82[ASN][1000 genomes]
rs3745446	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3826757	0.85[ASN][1000 genomes]
rs4801526	0.91[ASN][1000 genomes]
rs523509	0.93[ASN][1000 genomes]
rs575274	0.91[EUR][1000 genomes]
rs57544196	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs584405	0.87[ASN][1000 genomes]
rs58490076	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs610811	0.91[EUR][1000 genomes]
rs617073	0.87[ASN][1000 genomes]
rs648651	0.81[ASN][1000 genomes]
rs681804	0.87[ASN][1000 genomes]
rs73613281	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56163400-56167800	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr19:56163400-56168000	Active TSS	H9 Cell Line	embryonic stem cell
3	chr19:56163400-56168200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:56163600-56167800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr19:56163600-56167800	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr19:56163600-56168000	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr19:56164200-56168000	Active TSS	H1 Cell Line	embryonic stem cell
8	chr19:56164400-56166400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr19:56164400-56167000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr19:56164400-56167200	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr19:56164400-56167200	Active TSS	NHEK	skin
12	chr19:56164400-56167600	Active TSS	Hela-S3	cervix
13	chr19:56164400-56167800	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr19:56164400-56168000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr19:56164400-56168000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr19:56164400-56168400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr19:56164600-56167000	Active TSS	Rectal Smooth Muscle	rectum
18	chr19:56164600-56167200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr19:56164600-56167200	Active TSS	Colon Smooth Muscle	Colon
20	chr19:56164600-56167200	Active TSS	Osteobl	bone
21	chr19:56164600-56167400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:56164600-56167400	Active TSS	Fetal Brain Female	brain
23	chr19:56164600-56167600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr19:56164600-56167600	Active TSS	Psoas Muscle	Psoas
25	chr19:56164600-56167800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr19:56164600-56167800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:56164800-56166600	Active TSS	Stomach Smooth Muscle	stomach
28	chr19:56164800-56167000	Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr19:56164800-56167000	Active TSS	Duodenum Mucosa	Duodenum
30	chr19:56164800-56167000	Active TSS	Right Ventricle	heart
31	chr19:56164800-56167000	Active TSS	Thymus	Thymus
32	chr19:56164800-56167000	Active TSS	A549	lung
33	chr19:56164800-56167000	Active TSS	Dnd41	blood
34	chr19:56164800-56167200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr19:56164800-56167200	Active TSS	Brain Cingulate Gyrus	brain
36	chr19:56164800-56167200	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr19:56164800-56167200	Active TSS	Placenta	Placenta
38	chr19:56164800-56167200	Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr19:56164800-56167200	Active TSS	Monocytes-CD14+_RO01746	blood
40	chr19:56164800-56167200	Active TSS	NH-A	brain
41	chr19:56164800-56167400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr19:56164800-56167400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr19:56164800-56167400	Active TSS	Fetal Intestine Large	intestine
44	chr19:56164800-56167400	Active TSS	HSMM	muscle
45	chr19:56164800-56167600	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr19:56164800-56167600	Active TSS	NHLF	lung
47	chr19:56164800-56167800	Active TSS	Fetal Lung	lung
48	chr19:56164800-56167800	Active TSS	HMEC	breast
49	chr19:56164800-56168000	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr19:56164800-56168000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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