Variant report

Variant	rs12979040
Chromosome Location	chr19:36681418-36681419
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:54)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:54 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr19:36681404-36681682	A549	lung:	n/a	n/a
2	RAD21	chr19:36681383-36681685	MCF-7	breast:	n/a	n/a
3	CTCF	chr19:36681417-36681631	HepG2	liver:	n/a	n/a
4	SMC3	chr19:36681369-36681710	Hela-S3	cervix:	n/a	n/a
5	SMC3	chr19:36681409-36681699	HepG2	liver:	n/a	n/a
6	CTCF	chr19:36681369-36681807	K562	blood:	n/a	n/a
7	RAD21	chr19:36681410-36681717	K562	blood:	n/a	n/a
8	CTCF	chr19:36681355-36681704	K562	blood:	n/a	n/a
9	CTCF	chr19:36681353-36681710	IMR90	lung:	n/a	n/a
10	CTCF	chr19:36681401-36681698	HCT-116	colon:	n/a	n/a
11	CTCF	chr19:36681400-36681550	HMEC	breast:	n/a	n/a
12	CTCF	chr19:36681380-36681530	GM12866	blood:	n/a	n/a
13	RAD21	chr19:36681314-36681754	HepG2	liver:	n/a	n/a
14	RAD21	chr19:36681326-36681794	HCT-116	colon:	n/a	n/a
15	ZNF384	chr19:36681317-36681716	K562	blood:	n/a	n/a
16	RAD21	chr19:36681342-36681700	HepG2	liver:	n/a	n/a
17	RAD21	chr19:36681390-36681677	HCT-116	colon:	n/a	n/a
18	CTCF	chr19:36681356-36681715	GM12878	blood:	n/a	n/a
19	CTCF	chr19:36681405-36681587	SK-N-SH_RA	brain:	n/a	n/a
20	RAD21	chr19:36681376-36681698	SK-N-SH_RA	brain:	n/a	n/a
21	CTCF	chr19:36681408-36681749	A549	lung:	n/a	n/a
22	RAD21	chr19:36681352-36681747	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr19:36681380-36681530	HFF	foreskin:	n/a	n/a
24	RAD21	chr19:36681359-36681637	GM12878	blood:	n/a	n/a
25	CTCF	chr19:36681357-36681649	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr19:36681418-36681579	A549	lung:	n/a	n/a
27	RAD21	chr19:36681365-36681795	SK-N-SH	brain:	n/a	n/a
28	ZNF384	chr19:36681348-36681707	GM12878	blood:	n/a	n/a
29	RAD21	chr19:36681370-36681726	HepG2	liver:	n/a	n/a
30	RAD21	chr19:36681355-36681692	ECC-1	luminal epithelium:	n/a	n/a
31	CTCF	chr19:36681412-36681658	HUVEC	blood vessel:	n/a	n/a
32	RAD21	chr19:36681353-36681748	A549	lung:	n/a	n/a
33	RAD21	chr19:36681400-36681742	H1-hESC	embryonic stem cell:	n/a	n/a
34	RAD21	chr19:36681414-36681684	GM12878	blood:	n/a	n/a
35	CTCF	chr19:36681416-36681639	H1-hESC	embryonic stem cell:	n/a	n/a
36	PRDM1	chr19:36681409-36681710	Hela-S3	cervix:	n/a	chr19:36681584-36681599
37	RFX5	chr19:36681377-36681792	SK-N-SH	brain:	n/a	n/a
38	RAD21	chr19:36681361-36681737	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr19:36681360-36681805	SK-N-SH	brain:	n/a	n/a
40	RAD21	chr19:36681321-36681713	H1-hESC	embryonic stem cell:	n/a	n/a
41	SMC3	chr19:36681402-36681701	K562	blood:	n/a	n/a
42	SMC3	chr19:36681407-36681651	GM12878	blood:	n/a	n/a
43	RAD21	chr19:36681381-36681690	ECC-1	luminal epithelium:	n/a	n/a
44	RAD21	chr19:36681355-36681666	SK-N-SH_RA	brain:	n/a	n/a
45	CTCF	chr19:36681390-36681638	HepG2	liver:	n/a	n/a
46	CTCF	chr19:36681327-36681872	A549	lung:	n/a	n/a
47	RAD21	chr19:36681362-36681742	IMR90	lung:	n/a	n/a
48	RAD21	chr19:36681367-36681722	GM12878	blood:	n/a	n/a
49	YY1	chr19:36681345-36681623	H1-hESC	embryonic stem cell:	n/a	n/a
50	SMC3	chr19:36681332-36681785	SK-N-SH	brain:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36680583..36682778-chr19:36705094..36707466,2	K562	blood:
2	chr19:36679317..36682281-chr19:36704526..36707611,3	MCF-7	breast:

No data

Variant related genes	Relation type
RN7SL287P	TF binding region
ENSG00000167635	Chromatin interaction
ENSG00000196357	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12972727	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12979571	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12979812	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12981691	0.91[AMR][1000 genomes]
rs12982577	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12985315	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16960884	1.00[EUR][1000 genomes]
rs16970932	1.00[EUR][1000 genomes]
rs34072267	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34242075	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34423559	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34521310	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34527953	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34579456	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35342321	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35747960	0.95[EUR][1000 genomes]
rs35813323	1.00[EUR][1000 genomes]
rs35927732	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35989746	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71354126	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71354130	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7258851	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8104927	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	esv2752541	chr19:36563057-36690874	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv579425	chr19:36643695-36685753	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36653200-36684600	Weak transcription	Aorta	Aorta
2	chr19:36661800-36684600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:36661800-36686800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr19:36662000-36684800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr19:36669200-36685000	Weak transcription	Stomach Mucosa	stomach
6	chr19:36669600-36704800	Weak transcription	Psoas Muscle	Psoas
7	chr19:36673800-36704800	Weak transcription	Fetal Kidney	kidney
8	chr19:36674000-36685200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr19:36674000-36704800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr19:36674200-36685000	Weak transcription	Fetal Thymus	thymus
11	chr19:36674200-36685600	Weak transcription	Colon Smooth Muscle	Colon
12	chr19:36674200-36687200	Weak transcription	GM12878-XiMat	blood
13	chr19:36674400-36682600	Weak transcription	Lung	lung
14	chr19:36674400-36683200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr19:36674400-36684200	Weak transcription	HUVEC	blood vessel
16	chr19:36674400-36684600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr19:36674400-36684600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr19:36674400-36684600	Weak transcription	Fetal Intestine Large	intestine
19	chr19:36674400-36684600	Weak transcription	Left Ventricle	heart
20	chr19:36674400-36684600	Weak transcription	Pancreas	Pancrea
21	chr19:36674400-36684800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:36674400-36684800	Weak transcription	Right Ventricle	heart
23	chr19:36674400-36685200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr19:36674400-36685200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr19:36674400-36690000	Weak transcription	NHDF-Ad	bronchial
26	chr19:36674400-36704600	Weak transcription	Fetal Brain Male	brain
27	chr19:36674600-36682200	Weak transcription	Fetal Muscle Leg	muscle
28	chr19:36674600-36682400	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr19:36674600-36682400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr19:36674600-36682400	Weak transcription	Brain Hippocampus Middle	brain
31	chr19:36674600-36682400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr19:36674600-36682400	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr19:36674600-36682600	Weak transcription	Liver	Liver
34	chr19:36674600-36682600	Weak transcription	Brain Angular Gyrus	brain
35	chr19:36674600-36682800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr19:36674600-36682800	Weak transcription	Fetal Intestine Small	intestine
37	chr19:36674600-36683400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr19:36674600-36683400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr19:36674600-36683600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr19:36674600-36683600	Weak transcription	Fetal Brain Female	brain
41	chr19:36674600-36683800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr19:36674600-36684400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:36674600-36684400	Weak transcription	Ovary	ovary
44	chr19:36674600-36684600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:36674600-36684600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr19:36674600-36684600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:36674600-36684600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr19:36674600-36684600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr19:36674600-36684600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr19:36674600-36684600	Weak transcription	Primary B cells from peripheral blood	blood

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