Variant report

Variant	rs12983085
Chromosome Location	chr19:55768827-55768828
allele	A/C
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	UBTF	chr19:55768656-55771041	K562	blood:	n/a	n/a
2	SIN3AK20	chr19:55768209-55771137	PANC-1	pancreas:	n/a	n/a
3	MYC	chr19:55768210-55769120	K562	blood:	n/a	chr19:55768523-55768532
4	ELF1	chr19:55768721-55769107	K562	blood:	n/a	n/a
5	MAX	chr19:55767856-55769190	HepG2	liver:	n/a	chr19:55768523-55768532
6	MYC	chr19:55768801-55768946	GM12878	blood:	n/a	n/a
7	E2F6	chr19:55768165-55769427	K562	blood:	n/a	chr19:55769298-55769310 chr19:55768957-55768968
8	BHLHE40	chr19:55768196-55769177	K562	blood:	n/a	n/a
9	MAX	chr19:55767908-55769051	HepG2	liver:	n/a	chr19:55768523-55768532
10	EGR1	chr19:55768751-55769146	K562	blood:	n/a	n/a
11	MAX	chr19:55768687-55769185	A549	lung:	n/a	n/a
12	POLR2A	chr19:55768453-55769545	GM12878	blood:	n/a	n/a
13	SIN3AK20	chr19:55768819-55769103	H1-hESC	embryonic stem cell:	n/a	n/a
14	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
15	USF2	chr19:55768443-55769396	GM12878	blood:	n/a	n/a
16	MXI1	chr19:55768818-55769163	Hela-S3	cervix:	n/a	n/a
17	BHLHE40	chr19:55768690-55769575	GM12878	blood:	n/a	n/a
18	MYC	chr19:55768785-55768838	MCF10A-Er-Src	breast:	n/a	n/a
19	PML	chr19:55768375-55769354	GM12878	blood:	n/a	chr19:55769260-55769268
20	SIN3AK20	chr19:55768363-55769197	K562	blood:	n/a	n/a
21	POLR2A	chr19:55768452-55769359	GM12878	blood:	n/a	n/a
22	ETS1	chr19:55768772-55769045	K562	blood:	n/a	n/a
23	POLR2A	chr19:55768623-55769094	K562	blood:	n/a	n/a
24	MAX	chr19:55768392-55769255	K562	blood:	n/a	chr19:55768523-55768532
25	POLR2A	chr19:55768806-55769160	K562	blood:	n/a	n/a
26	SIN3AK20	chr19:55768581-55769237	MCF-7	breast:	n/a	n/a
27	POLR2A	chr19:55768098-55769444	HL-60	blood:	n/a	n/a
28	E2F6	chr19:55768790-55769094	K562	blood:	n/a	chr19:55768957-55768968
29	MAX	chr19:55768261-55769239	K562	blood:	n/a	chr19:55768523-55768532
30	SMARCB1	chr19:55768503-55771011	Hela-S3	cervix:	n/a	n/a
31	MAX	chr19:55767994-55769837	K562	blood:	n/a	chr19:55769750-55769759 chr19:55768523-55768532
32	MAZ	chr19:55768682-55771570	IMR90	lung:	n/a	chr19:55770411-55770421 chr19:55769750-55769759
33	MYC	chr19:55768179-55769110	NB4	blood:	n/a	chr19:55768523-55768532
34	MYC	chr19:55768256-55769103	K562	blood:	n/a	chr19:55768523-55768532
35	POLR2A	chr19:55768814-55769324	U87	brain:	n/a	n/a
36	MYC	chr19:55768470-55769220	K562	blood:	n/a	chr19:55768523-55768532
37	MYC	chr19:55768819-55769063	MCF-7	breast:	n/a	n/a
38	MAX	chr19:55768803-55769044	H1-hESC	embryonic stem cell:	n/a	n/a
39	MAX	chr19:55768756-55769198	SK-N-SH	brain:	n/a	n/a
40	SIN3AK20	chr19:55768737-55769175	PFSK-1	brain:	n/a	n/a
41	MAX	chr19:55768761-55769186	H1-hESC	embryonic stem cell:	n/a	n/a
42	WRNIP1	chr19:55764368-55769616	GM12878	blood:	n/a	n/a
43	MAZ	chr19:55768527-55771142	GM12878	blood:	n/a	chr19:55770411-55770421 chr19:55769750-55769759
44	TBL1XR1	chr19:55768607-55768912	GM12878	blood:	n/a	n/a
45	MAX	chr19:55768081-55769292	NB4	blood:	n/a	chr19:55768523-55768532
46	E2F6	chr19:55768790-55769102	K562	blood:	n/a	chr19:55768957-55768968
47	SIN3AK20	chr19:55768750-55769090	K562	blood:	n/a	n/a
48	MAZ	chr19:55768734-55769190	K562	blood:	n/a	n/a
49	MAX	chr19:55768705-55769151	H1-hESC	embryonic stem cell:	n/a	n/a
50	RCOR1	chr19:55768381-55771561	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:55767248..55770437-chr19:55917297..55920206,6	MCF-7	breast:
2	chr19:55768392..55770990-chr19:55864103..55865699,2	MCF-7	breast:
3	chr19:55718690..55723182-chr19:55767265..55771415,7	MCF-7	breast:
4	chr19:55767441..55773483-chr19:55893952..55900251,14	MCF-7	breast:
5	chr19:55690523..55693470-chr19:55767618..55771014,3	K562	blood:
6	chr19:55764902..55773441-chr19:55891413..55900303,21	K562	blood:
7	chr19:55763551..55774813-chr19:55891413..55900376,23	K562	blood:
8	chr19:55767441..55772178-chr19:55789060..55793175,7	MCF-7	breast:
9	chr19:55726487..55728063-chr19:55766262..55769057,2	MCF-7	breast:
10	chr19:55766579..55768954-chr19:55914081..55916884,2	K562	blood:
11	chr19:55767517..55772398-chr19:55789828..55793738,15	K562	blood:
12	chr19:55768444..55771983-chr19:55917721..55920953,5	K562	blood:
13	chr19:55724113..55730012-chr19:55766381..55773608,39	K562	blood:
14	chr19:55750475..55753226-chr19:55768525..55770423,2	MCF-7	breast:
15	chr19:55720878..55730679-chr19:55764402..55774570,47	K562	blood:
16	chr19:55756546..55759225-chr19:55768234..55771187,4	MCF-7	breast:
17	chr19:55768430..55771983-chr19:55917442..55920696,5	K562	blood:
18	chr19:55732279..55738678-chr19:55765531..55770516,7	K562	blood:
19	chr19:55767479..55769662-chr19:55951902..55953549,2	MCF-7	breast:
20	chr19:55767450..55771021-chr19:55880319..55882334,3	MCF-7	breast:
21	chr19:55764275..55774774-chr19:55790059..55800763,24	K562	blood:

Variant related genes	Relation type
PPP6R1	TF binding region
ENSG00000160471	Chromatin interaction
ENSG00000080031	Chromatin interaction
ENSG00000267649	Chromatin interaction
ENSG00000133265	Chromatin interaction
ENSG00000269808	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000160469	Chromatin interaction
ENSG00000105063	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000095752	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10403164	0.96[MEX][hapmap];0.84[AMR][1000 genomes]
rs10403571	0.83[AMR][1000 genomes]
rs10412187	0.96[MEX][hapmap];0.84[AMR][1000 genomes]
rs10414721	0.86[AMR][1000 genomes]
rs10424537	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11880758	0.84[AMR][1000 genomes]
rs11880781	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12974813	0.82[JPT][hapmap]
rs3745920	0.82[GIH][hapmap]
rs4072920	0.87[AMR][1000 genomes]
rs4473307	0.89[CEU][hapmap];0.88[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4806656	0.96[MEX][hapmap]
rs4806657	0.81[AMR][1000 genomes]
rs62126354	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67351527	0.93[AMR][1000 genomes];0.86[EUR][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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55758400-55769000	Weak transcription	Aorta	Aorta
2	chr19:55764200-55769200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
3	chr19:55764200-55769600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr19:55764200-55769600	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr19:55764200-55769600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:55764400-55769200	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr19:55764400-55769400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr19:55764600-55769400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr19:55764600-55769600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
10	chr19:55764600-55769600	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr19:55764600-55769600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:55764800-55769800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
13	chr19:55764800-55770400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:55765200-55769800	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr19:55765400-55769800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr19:55765800-55769400	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr19:55766000-55770600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr19:55766400-55769000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
19	chr19:55766800-55769200	Flanking Active TSS	Brain Cingulate Gyrus	brain
20	chr19:55766800-55769400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr19:55766800-55769800	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr19:55767000-55769200	Flanking Active TSS	Brain Angular Gyrus	brain
23	chr19:55767000-55769600	Flanking Active TSS	Colonic Mucosa	Colon
24	chr19:55767200-55769200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr19:55767200-55769200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr19:55767200-55769200	Flanking Active TSS	Stomach Mucosa	stomach
27	chr19:55767600-55769000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr19:55767600-55769200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr19:55767600-55769200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:55767600-55769200	Flanking Active TSS	Osteobl	bone
31	chr19:55767600-55769400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
32	chr19:55767800-55769000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr19:55767800-55769000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
34	chr19:55767800-55769200	Flanking Active TSS	NH-A	brain
35	chr19:55767800-55769400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr19:55767800-55769400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:55767800-55769400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr19:55767800-55769400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr19:55767800-55769600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:55768000-55769000	Flanking Active TSS	Colon Smooth Muscle	Colon
41	chr19:55768000-55769000	Enhancers	Placenta Amnion	Placenta Amnion
42	chr19:55768000-55769200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr19:55768000-55769200	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr19:55768000-55769400	Flanking Active TSS	Right Ventricle	heart
45	chr19:55768000-55769400	Flanking Active TSS	HMEC	breast
46	chr19:55768000-55769600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:55768200-55769000	Flanking Active TSS	Fetal Brain Male	brain
48	chr19:55768200-55769000	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
49	chr19:55768200-55769200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:55768200-55769200	Flanking Active TSS	NHEK	skin

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