Variant report

Variant	rs310474
Chromosome Location	chr19:56155236-56155237
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	MAX	chr19:56151221-56155795	A549	lung:	n/a	chr19:56155426-56155435 chr19:56151539-56151548 chr19:56151539-56151549 chr19:56151539-56151549 chr19:56155425-56155436 chr19:56151538-56151549
2	POLR2A	chr19:56151273-56155759	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr19:56150319-56156666	Hela-S3	cervix:	n/a	n/a
4	E2F6	chr19:56154766-56155311	K562	blood:	n/a	chr19:56155023-56155033
5	BCL3	chr19:56154437-56155251	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:56150228-56156269	GM12891	blood:	n/a	n/a
7	MAX	chr19:56153938-56155724	K562	blood:	n/a	chr19:56155426-56155435 chr19:56155425-56155436
8	SIN3AK20	chr19:56154481-56155266	SK-N-SH	brain:	n/a	n/a
9	GABPA	chr19:56154541-56155329	MCF-7	breast:	n/a	n/a
10	GATA3	chr19:56154034-56155247	A549	lung:	n/a	n/a
11	EGR1	chr19:56154109-56155347	HCT-116	colon:	n/a	chr19:56154853-56154863
12	CEBPD	chr19:56154705-56155399	HepG2	liver:	n/a	n/a
13	POLR2A	chr19:56150192-56156534	GM12878	blood:	n/a	n/a
14	REST	chr19:56154533-56155318	A549	lung:	n/a	n/a
15	POLR2A	chr19:56155154-56155488	K562	blood:	n/a	n/a
16	MAX	chr19:56153911-56155790	HepG2	liver:	n/a	chr19:56155426-56155435 chr19:56155425-56155436
17	MAX	chr19:56154061-56155507	Hela-S3	cervix:	n/a	chr19:56155426-56155435 chr19:56155425-56155436
18	POLR2A	chr19:56153839-56155319	A549	lung:	n/a	n/a
19	EGR1	chr19:56155202-56155453	K562	blood:	n/a	chr19:56155361-56155371
20	ZBTB7A	chr19:56155165-56155530	K562	blood:	n/a	chr19:56155265-56155274
21	TAF1	chr19:56154733-56155525	HepG2	liver:	n/a	n/a
22	POLR2A	chr19:56153442-56155799	K562	blood:	n/a	n/a
23	POLR2A	chr19:56153870-56155909	GM12892	blood:	n/a	n/a
24	POLR2A	chr19:56153525-56155261	MCF-7	breast:	n/a	n/a
25	POLR2A	chr19:56154287-56155832	PFSK-1	brain:	n/a	n/a
26	CHD2	chr19:56151532-56155316	Hela-S3	cervix:	n/a	chr19:56154963-56154973 chr19:56152366-56152373
27	POLR2A	chr19:56149778-56157300	PANC-1	pancreas:	n/a	n/a
28	POLR2A	chr19:56153491-56155368	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAX	chr19:56153814-56155640	HCT-116	colon:	n/a	chr19:56155426-56155435 chr19:56155425-56155436
30	ESRRA	chr19:56154205-56155663	GM12878	blood:	n/a	chr19:56155635-56155653
31	MAX	chr19:56153939-56155716	MCF-7	breast:	n/a	chr19:56155426-56155435 chr19:56155425-56155436
32	POLR2A	chr19:56154069-56155550	GM12878	blood:	n/a	n/a
33	POLR2A	chr19:56150010-56156634	MCF10A-Er-Src	breast:	n/a	n/a
34	SP1	chr19:56154387-56155302	A549	lung:	n/a	chr19:56154963-56154975 chr19:56154964-56154973 chr19:56154965-56154974 chr19:56154964-56154973 chr19:56154963-56154975 chr19:56154964-56154974
35	POLR2A	chr19:56151299-56155891	MCF-7	breast:	n/a	n/a
36	POLR2A	chr19:56155158-56155448	A549	lung:	n/a	n/a
37	POLR2A	chr19:56154040-56155525	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr19:56155147-56155605	SK-N-SH	brain:	n/a	n/a
39	TAF1	chr19:56154590-56155271	A549	lung:	n/a	n/a
40	POLR2A	chr19:56151325-56156943	GM19099	blood:	n/a	n/a
41	POLR2A	chr19:56150270-56155844	PANC-1	pancreas:	n/a	n/a
42	TAF1	chr19:56154668-56155458	ECC-1	luminal epithelium:	n/a	n/a
43	ZNF263	chr19:56154054-56156500	HEK293-T-REx	kidney:	n/a	n/a
44	PML	chr19:56153908-56155669	GM12878	blood:	n/a	chr19:56155008-56155016
45	POLR2A	chr19:56151350-56155716	GM18526	blood:	n/a	n/a
46	MAX	chr19:56154677-56155555	NB4	blood:	n/a	chr19:56155426-56155435 chr19:56155425-56155436
47	POLR2A	chr19:56155193-56155516	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr19:56153363-56155275	ECC-1	luminal epithelium:	n/a	n/a
49	HMGN3	chr19:56154751-56155471	K562	blood:	n/a	n/a
50	POLR2A	chr19:56153995-56155449	GM10847	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:56154666..56155441-chr19:56164653..56165540,4	MCF-7	breast:
2	chr19:55996982..55998485-chr19:56153883..56155903,2	K562	blood:
3	chr19:56132811..56137423-chr19:56151241..56156557,5	MCF-7	breast:
4	chr19:55964915..55966958-chr19:56152410..56155336,2	K562	blood:
5	chr19:56154949..56157092-chr19:56632186..56634615,2	K562	blood:
6	chr19:56154222..56156750-chr19:56202512..56205168,2	K562	blood:
7	chr19:56110029..56112023-chr19:56153492..56156368,2	K562	blood:
8	chr19:56134500..56138557-chr19:56151822..56155582,4	K562	blood:
9	chr19:56154378..56155395-chr19:56164636..56165646,5	K562	blood:
10	chr19:56133203..56138391-chr19:56150309..56156340,8	K562	blood:
11	chr19:55917778..55920684-chr19:56153894..56155704,2	K562	blood:
12	chr19:56153424..56156443-chr19:56220513..56224838,3	K562	blood:
13	chr19:56154889..56155389-chr20:26189706..26190477,2	K562	blood:
14	chr19:55896816..55898587-chr19:56153997..56156129,2	MCF-7	breast:
15	chr19:56115086..56118069-chr19:56150430..56156112,7	MCF-7	breast:
16	chr19:55918058..55920032-chr19:56154826..56156476,2	MCF-7	breast:
17	chr19:55998666..56000299-chr19:56153756..56156154,2	K562	blood:
18	chr19:56152964..56155802-chr19:56186387..56188533,2	MCF-7	breast:

Variant related genes	Relation type
CCDC106	TF binding region
ENSG00000179954	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000063245	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000269574	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000090971	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000227195	Chromatin interaction
ENSG00000142409	Chromatin interaction
ENSG00000063241	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs310470	1.00[EUR][1000 genomes]
rs310471	1.00[EUR][1000 genomes]
rs507498	0.83[EUR][1000 genomes]
rs57063593	0.83[EUR][1000 genomes]
rs581023	0.84[EUR][1000 genomes]
rs600106	0.83[EUR][1000 genomes]
rs612211	0.89[EUR][1000 genomes]
rs636466	1.00[EUR][1000 genomes]
rs636467	1.00[EUR][1000 genomes]
rs637788	0.89[EUR][1000 genomes]
rs644230	0.89[EUR][1000 genomes]
rs679577	0.83[EUR][1000 genomes]
rs680444	0.83[EUR][1000 genomes]
rs681433	0.83[EUR][1000 genomes]
rs7246799	1.00[EUR][1000 genomes]
rs7251872	0.81[EUR][1000 genomes]
rs889091	0.89[EUR][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	nsv912503	chr19:56149077-56162776	Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
8	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56151600-56155600	Active TSS	Ovary	ovary
2	chr19:56151600-56155800	Active TSS	Fetal Kidney	kidney
3	chr19:56151600-56156000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr19:56151600-56156200	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr19:56151600-56156200	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr19:56151800-56155800	Active TSS	H9 Cell Line	embryonic stem cell
7	chr19:56151800-56156000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr19:56151800-56156000	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr19:56152000-56155800	Active TSS	H1 Cell Line	embryonic stem cell
10	chr19:56152200-56156000	Active TSS	Small Intestine	intestine
11	chr19:56152600-56156000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr19:56152800-56155800	Flanking Active TSS	Fetal Muscle Leg	muscle
13	chr19:56152800-56156000	Flanking Active TSS	Primary B cells from peripheral blood	blood
14	chr19:56153000-56155800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:56154400-56155400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:56154400-56155800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr19:56154400-56155800	Flanking Active TSS	Fetal Muscle Trunk	muscle
18	chr19:56154400-56156000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:56154400-56156000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:56154400-56156000	Flanking Active TSS	Placenta	Placenta
21	chr19:56154600-56155400	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr19:56154600-56155400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr19:56154600-56155600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:56154600-56156000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr19:56154600-56156000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr19:56154600-56156000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr19:56154800-56155400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr19:56154800-56155400	Active TSS	Primary monocytes fromperipheralblood	blood
29	chr19:56154800-56155400	Active TSS	Primary B cells from cord blood	blood
30	chr19:56154800-56155400	Active TSS	Primary T cells from cord blood	blood
31	chr19:56154800-56155400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr19:56154800-56155400	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr19:56154800-56155400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr19:56154800-56155400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr19:56154800-56155400	Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr19:56154800-56155400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr19:56154800-56155400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr19:56154800-56155400	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr19:56154800-56155400	Active TSS	Brain Anterior Caudate	brain
40	chr19:56154800-56155400	Active TSS	Brain Cingulate Gyrus	brain
41	chr19:56154800-56155400	Active TSS	Brain Hippocampus Middle	brain
42	chr19:56154800-56155400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:56154800-56155400	Active TSS	Colonic Mucosa	Colon
44	chr19:56154800-56155400	Active TSS	Duodenum Mucosa	Duodenum
45	chr19:56154800-56155400	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr19:56154800-56155400	Enhancers	Fetal Brain Male	brain
47	chr19:56154800-56155400	Active TSS	Fetal Brain Female	brain
48	chr19:56154800-56155400	Active TSS	Fetal Intestine Small	intestine
49	chr19:56154800-56155400	Active TSS	Fetal Stomach	stomach
50	chr19:56154800-56155400	Active TSS	Rectal Mucosa Donor 31	rectum

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