Variant report

Variant	rs11880758
Chromosome Location	chr19:55771088-55771089
allele	C/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	POLR2A	chr19:55769871-55771537	GM12892	blood:	n/a	n/a
2	EP300	chr19:55770056-55771101	HepG2	liver:	n/a	chr19:55770440-55770456 chr19:55770322-55770338
3	POLR2A	chr19:55770059-55771242	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr19:55769976-55771235	PBDE	blood:	n/a	n/a
5	POLR2A	chr19:55769949-55771495	K562	blood:	n/a	n/a
6	ELF1	chr19:55770115-55771182	MCF-7	breast:	n/a	chr19:55770446-55770458 chr19:55770320-55770332 chr19:55770333-55770345
7	POLR2A	chr19:55769936-55771536	U87	brain:	n/a	n/a
8	SIN3AK20	chr19:55768209-55771137	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr19:55769829-55771415	GM19099	blood:	n/a	n/a
10	CHD1	chr19:55770247-55771301	GM12878	blood:	n/a	chr19:55770450-55770460
11	JUND	chr19:55770310-55771178	SK-N-SH	brain:	n/a	chr19:55770747-55770761 chr19:55770448-55770457 chr19:55770639-55770653
12	POLR2A	chr19:55769721-55771109	GM18526	blood:	n/a	n/a
13	ELF1	chr19:55770461-55771097	A549	lung:	n/a	n/a
14	POLR2A	chr19:55770078-55771230	U87	brain:	n/a	n/a
15	SIN3AK20	chr19:55770111-55771266	MCF-7	breast:	n/a	n/a
16	POLR2A	chr19:55770098-55771252	GM12878	blood:	n/a	n/a
17	PBX3	chr19:55769993-55771121	SK-N-SH	brain:	n/a	n/a
18	EP300	chr19:55770213-55771160	SK-N-SH	brain:	n/a	chr19:55770440-55770456 chr19:55770322-55770338
19	REST	chr19:55769162-55771383	H1-neurons	neurons:	n/a	chr19:55769581-55769594 chr19:55769348-55769368
20	POLR2A	chr19:55769961-55771209	MCF10A-Er-Src	breast:	n/a	n/a
21	SPI1	chr19:55770017-55771115	HL-60	blood:	n/a	n/a
22	POLR2A	chr19:55769880-55771250	K562	blood:	n/a	n/a
23	SP1	chr19:55770047-55771156	H1-hESC	embryonic stem cell:	n/a	chr19:55770448-55770460 chr19:55770410-55770422 chr19:55770450-55770459 chr19:55770449-55770458 chr19:55770411-55770420 chr19:55770445-55770459 chr19:55770449-55770459 chr19:55770411-55770425 chr19:55770448-55770460 chr19:55770450-55770459 chr19:55770449-55770459 chr19:55770410-55770422 chr19:55770411-55770421 chr19:55770412-55770421
24	PML	chr19:55770051-55771129	K562	blood:	n/a	n/a
25	POLR2A	chr19:55769907-55771115	ProgFib	skin:	n/a	n/a
26	ELF1	chr19:55770036-55771138	MCF-7	breast:	n/a	chr19:55770446-55770458 chr19:55770320-55770332 chr19:55770073-55770085 chr19:55770333-55770345
27	POLR2A	chr19:55770003-55771340	PFSK-1	brain:	n/a	n/a
28	MTA3	chr19:55769866-55771413	GM12878	blood:	n/a	n/a
29	CREB1	chr19:55770119-55771094	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr19:55770095-55771096	HepG2	liver:	n/a	n/a
31	POLR2A	chr19:55770061-55771183	SK-N-SH	brain:	n/a	n/a
32	TCF12	chr19:55769895-55771125	ECC-1	luminal epithelium:	n/a	chr19:55770442-55770449
33	YY1	chr19:55770119-55771101	SK-N-SH	brain:	n/a	chr19:55770521-55770530 chr19:55770449-55770458 chr19:55770521-55770532 chr19:55770404-55770418
34	GABPA	chr19:55770128-55771135	SK-N-SH	brain:	n/a	chr19:55770536-55770547 chr19:55770476-55770490 chr19:55770449-55770458 chr19:55770434-55770448 chr19:55770479-55770490
35	MAX	chr19:55769973-55771104	Hela-S3	cervix:	n/a	chr19:55770411-55770421
36	POLR2A	chr19:55769717-55771446	K562	blood:	n/a	n/a
37	BCLAF1	chr19:55770140-55771261	GM12878	blood:	n/a	chr19:55770438-55770451 chr19:55770521-55770534 chr19:55770523-55770532
38	MTA3	chr19:55770429-55771174	GM12878	blood:	n/a	n/a
39	GATA1	chr19:55770225-55771195	PBDE	blood:	n/a	chr19:55770377-55770390
40	POLR2A	chr19:55770124-55771106	K562	blood:	n/a	n/a
41	MAFK	chr19:55770146-55771170	Hela-S3	cervix:	n/a	n/a
42	MAX	chr19:55769961-55771207	ECC-1	luminal epithelium:	n/a	chr19:55770411-55770421
43	ELF1	chr19:55768714-55771361	GM12878	blood:	n/a	chr19:55769295-55769304 chr19:55770446-55770458 chr19:55770320-55770332 chr19:55770073-55770085 chr19:55769296-55769308 chr19:55770333-55770345
44	MAX	chr19:55769762-55771361	A549	lung:	n/a	chr19:55770411-55770421
45	POLR2A	chr19:55769716-55771437	NB4	blood:	n/a	n/a
46	CREB1	chr19:55770098-55771091	HepG2	liver:	n/a	n/a
47	POLR2A	chr19:55770001-55771401	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr19:55769645-55771461	GM18505	blood:	n/a	n/a
49	POLR2A	chr19:55770157-55771162	HepG2	liver:	n/a	n/a
50	SIN3AK20	chr19:55770112-55771100	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:55769670..55772442-chr19:55857047..55859778,2	K562	blood:
2	chr19:55770065..55771348-chr6:146056333..146057332,3	Hela-S3	cervix:
3	chr19:55769482..55772014-chr19:55910008..55913343,3	K562	blood:
4	chr19:55770321..55771177-chr5:39074454..39075248,2	Hela-S3	cervix:
5	chr19:55718690..55723182-chr19:55767265..55771415,7	MCF-7	breast:
6	chr19:55767441..55773483-chr19:55893952..55900251,14	MCF-7	breast:
7	chr19:55764902..55773441-chr19:55891413..55900303,21	K562	blood:
8	chr19:55770504..55771143-chr19:55865399..55866138,2	K562	blood:
9	chr19:55770686..55772282-chr19:55848676..55850979,2	K562	blood:
10	chr19:55763551..55774813-chr19:55891413..55900376,23	K562	blood:
11	chr19:55767441..55772178-chr19:55789060..55793175,7	MCF-7	breast:
12	chr19:55659384..55662186-chr19:55768928..55771825,2	K562	blood:
13	chr19:55768870..55771541-chr19:55794018..55795820,2	MCF-7	breast:
14	chr19:55769739..55771684-chr19:55850814..55852866,2	MCF-7	breast:
15	chr19:55770528..55773508-chr19:55917890..55920089,4	MCF-7	breast:
16	chr19:55727159..55729586-chr19:55769569..55772417,4	MCF-7	breast:
17	chr19:55769552..55771558-chr19:55896824..55899608,3	MCF-7	breast:
18	chr19:55770876..55771527-chr6:26205546..26206487,2	Hela-S3	cervix:
19	chr19:55657829..55659690-chr19:55769331..55772164,2	K562	blood:
20	chr19:55767517..55772398-chr19:55789828..55793738,15	K562	blood:
21	chr19:55768444..55771983-chr19:55917721..55920953,5	K562	blood:
22	chr19:55724113..55730012-chr19:55766381..55773608,39	K562	blood:
23	chr19:55736575..55738793-chr19:55769011..55771822,2	MCF-7	breast:
24	chr19:55720878..55730679-chr19:55764402..55774570,47	K562	blood:
25	chr19:55756546..55759225-chr19:55768234..55771187,4	MCF-7	breast:
26	chr19:55769028..55772088-chr19:55788931..55793273,6	MCF-7	breast:
27	chr19:55727366..55728438-chr19:55769798..55771153,4	Hela-S3	cervix:
28	chr19:55768430..55771983-chr19:55917442..55920696,5	K562	blood:
29	chr19:55689704..55692023-chr19:55769514..55771598,2	K562	blood:
30	chr19:55684145..55687547-chr19:55770390..55772403,3	K562	blood:
31	chr19:55726024..55729916-chr19:55768850..55773519,13	MCF-7	breast:
32	chr19:55764275..55774774-chr19:55790059..55800763,24	K562	blood:
33	chr19:55770986..55773436-chr19:55865504..55867451,2	K562	blood:

Variant related genes	Relation type
PPP6R1	TF binding region
ENSG00000269808	Chromatin interaction
ENSG00000133247	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000160471	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000267649	Chromatin interaction
ENSG00000105063	Chromatin interaction
ENSG00000164327	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000267093	Chromatin interaction
ENSG00000270638	Chromatin interaction
ENSG00000080031	Chromatin interaction
ENSG00000160469	Chromatin interaction
ENSG00000105048	Chromatin interaction
ENSG00000267531	Chromatin interaction
ENSG00000112425	Chromatin interaction
ENSG00000133265	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10403164	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10403571	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10411896	0.88[AFR][1000 genomes]
rs10412187	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10414721	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11880781	0.88[AMR][1000 genomes]
rs12983085	0.84[AMR][1000 genomes]
rs4072920	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806656	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4806657	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62126354	0.85[AMR][1000 genomes]
rs67351527	0.86[AMR][1000 genomes]
rs8105032	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912454	chr19:55725410-55783552	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
4	nsv912455	chr19:55725410-55879872	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
6	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
7	nsv912458	chr19:55763409-55823822	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55768400-55771400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr19:55768400-55771800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr19:55768600-55771200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:55768600-55771200	Active TSS	Ovary	ovary
5	chr19:55768800-55771200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:55768800-55771200	Active TSS	Esophagus	oesophagus
7	chr19:55768800-55771200	Active TSS	HSMM	muscle
8	chr19:55768800-55771200	Active TSS	NHDF-Ad	bronchial
9	chr19:55768800-55771400	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr19:55768800-55771400	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr19:55768800-55771400	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr19:55769000-55771200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr19:55769000-55771200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:55769000-55771200	Active TSS	Colon Smooth Muscle	Colon
15	chr19:55769000-55771200	Active TSS	Fetal Kidney	kidney
16	chr19:55769000-55771200	Active TSS	Rectal Smooth Muscle	rectum
17	chr19:55769000-55771200	Active TSS	HepG2	liver
18	chr19:55769000-55771400	Active TSS	H9 Cell Line	embryonic stem cell
19	chr19:55769000-55771400	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr19:55769000-55771600	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr19:55769200-55771200	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr19:55769200-55771200	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr19:55769200-55771200	Active TSS	Brain Anterior Caudate	brain
24	chr19:55769200-55771200	Active TSS	Brain Cingulate Gyrus	brain
25	chr19:55769200-55771200	Active TSS	Gastric	stomach
26	chr19:55769200-55771200	Active TSS	Placenta Amnion	Placenta Amnion
27	chr19:55769200-55771400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:55769200-55771400	Active TSS	Aorta	Aorta
29	chr19:55769200-55771400	Active TSS	Psoas Muscle	Psoas
30	chr19:55769400-55771200	Active TSS	H1 Cell Line	embryonic stem cell
31	chr19:55769400-55771200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:55769400-55771200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:55769400-55771200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr19:55769400-55771200	Active TSS	Brain Substantia Nigra	brain
35	chr19:55769400-55771200	Active TSS	Left Ventricle	heart
36	chr19:55769400-55771200	Active TSS	Pancreas	Pancrea
37	chr19:55769400-55771200	Active TSS	Right Ventricle	heart
38	chr19:55769400-55771200	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr19:55769400-55771200	Active TSS	Spleen	Spleen
40	chr19:55769400-55771200	Active TSS	Dnd41	blood
41	chr19:55769400-55771400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr19:55769600-55771200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr19:55769600-55771200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:55769600-55771200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr19:55769600-55771200	Active TSS	Colonic Mucosa	Colon
46	chr19:55769600-55771400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr19:55769800-55771200	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr19:55769800-55771200	Active TSS	Stomach Smooth Muscle	stomach
49	chr19:55770200-55771200	Active TSS	Brain Germinal Matrix	brain
50	chr19:55770400-55771200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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