Variant report

Variant	rs2607421
Chromosome Location	chr19:41277077-41277078
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41277058-41277197	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:41276976-41277286	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:41276976-41277174	HCT-116	colon:	n/a	n/a
4	POLR2A	chr19:41276955-41277280	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr19:41277019-41277225	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr19:41276719-41277315	H1-hESC	embryonic stem cell:	n/a	n/a
7	HEY1	chr19:41276981-41277250	HepG2	liver:	n/a	n/a
8	POLR2A	chr19:41276985-41277209	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr19:41276992-41277218	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr19:41277061-41277317	HepG2	liver:	n/a	n/a
11	POLR2A	chr19:41276795-41277456	SK-N-MC	brain:	n/a	n/a
12	POLR2A	chr19:41277062-41277203	A549	lung:	n/a	n/a
13	POLR2A	chr19:41276998-41277282	HepG2	liver:	n/a	n/a
14	POLR2A	chr19:41277024-41277200	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr19:41276998-41277276	Raji	blood:	n/a	n/a
16	NFYB	chr19:41277075-41277760	K562	blood:	n/a	chr19:41277527-41277542 chr19:41277486-41277501
17	POLR2A	chr19:41277041-41277217	HepG2	liver:	n/a	n/a
18	ELF1	chr19:41276977-41277352	K562	blood:	n/a	n/a
19	POLR2A	chr19:41276923-41277202	HUVEC	blood vessel:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41276921..41279823-chr19:41282678..41284570,2	MCF-7	breast:
2	chr19:41274845..41278396-chr19:41279079..41284996,6	K562	blood:
3	chr19:41267917..41272263-chr19:41274538..41279747,5	K562	blood:

No data

Variant related genes	Relation type
MIA-RAB4B	TF binding region
MIA	TF binding region
ENSG00000077312	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000261857	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs13108	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17726258	0.87[ASN][1000 genomes]
rs2230694	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2233153	0.88[ASN][1000 genomes]
rs2233154	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2233156	0.88[ASN][1000 genomes]
rs2233159	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2249854	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279699	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2545760	0.91[ASN][1000 genomes]
rs2545777	0.99[ASN][1000 genomes]
rs2545778	0.99[ASN][1000 genomes]
rs2604876	1.00[ASN][1000 genomes]
rs2604877	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2604909	0.94[ASN][1000 genomes]
rs2604910	0.94[ASN][1000 genomes]
rs2604911	0.94[ASN][1000 genomes]
rs2607411	0.98[ASN][1000 genomes]
rs2607412	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2607413	0.98[ASN][1000 genomes]
rs2607416	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2607419	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607422	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607423	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607425	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607426	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2644917	0.97[ASN][1000 genomes]
rs34842744	0.94[ASN][1000 genomes]
rs56891752	0.99[ASN][1000 genomes]
rs60533951	0.95[ASN][1000 genomes]
rs8107978	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8109099	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1802033	chr19:41256131-41284240	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	40 gene(s)	inside rSNPs	diseases
2	esv1801805	chr19:41256581-41284363	Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	37 gene(s)	inside rSNPs	diseases
3	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41258000-41283000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:41260600-41277200	Strong transcription	Fetal Brain Female	brain
3	chr19:41260800-41283200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:41261800-41278200	Strong transcription	Fetal Stomach	stomach
5	chr19:41261800-41282800	Weak transcription	Right Atrium	heart
6	chr19:41264600-41278000	Strong transcription	A549	lung
7	chr19:41270400-41282600	Weak transcription	Fetal Brain Male	brain
8	chr19:41271800-41279800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr19:41271800-41279800	Weak transcription	HMEC	breast
10	chr19:41271800-41282600	Weak transcription	Fetal Kidney	kidney
11	chr19:41271800-41282600	Weak transcription	HSMM	muscle
12	chr19:41271800-41283000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr19:41272000-41279400	Weak transcription	Ovary	ovary
14	chr19:41272000-41280400	Weak transcription	NHEK	skin
15	chr19:41272000-41280600	Weak transcription	NH-A	brain
16	chr19:41272000-41281200	Weak transcription	Osteobl	bone
17	chr19:41272000-41282600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr19:41272000-41282600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr19:41272000-41282600	Weak transcription	Brain Angular Gyrus	brain
20	chr19:41272000-41282600	Weak transcription	HUVEC	blood vessel
21	chr19:41272000-41282800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr19:41272000-41282800	Weak transcription	Psoas Muscle	Psoas
23	chr19:41272000-41282800	Weak transcription	Small Intestine	intestine
24	chr19:41272000-41282800	Weak transcription	NHDF-Ad	bronchial
25	chr19:41272200-41280800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr19:41272200-41280800	Weak transcription	Stomach Mucosa	stomach
27	chr19:41272200-41281200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr19:41272200-41281200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr19:41272200-41281200	Weak transcription	K562	blood
30	chr19:41272200-41282600	Weak transcription	Fetal Lung	lung
31	chr19:41272200-41282600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr19:41272200-41282600	Weak transcription	Dnd41	blood
33	chr19:41272200-41282600	Weak transcription	HSMMtube	muscle
34	chr19:41272200-41282600	Weak transcription	NHLF	lung
35	chr19:41272200-41282800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr19:41272200-41282800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr19:41272200-41282800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr19:41272200-41282800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:41272200-41282800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr19:41272200-41282800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr19:41272200-41282800	Weak transcription	Aorta	Aorta
42	chr19:41272200-41282800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr19:41272200-41282800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:41272200-41282800	Weak transcription	Brain Substantia Nigra	brain
45	chr19:41272200-41282800	Weak transcription	Esophagus	oesophagus
46	chr19:41272200-41282800	Weak transcription	Gastric	stomach
47	chr19:41272200-41282800	Weak transcription	Left Ventricle	heart
48	chr19:41272200-41282800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr19:41272200-41282800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr19:41272200-41282800	Weak transcription	Hela-S3	cervix

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