Variant report

Variant	rs12977821
Chromosome Location	chr19:39337442-39337443
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39337416-39343742	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr19:39337415-39337552	MCF-7	breast:	n/a	n/a
3	POLR2A	chr19:39332423-39344383	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:39337394-39343937	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr19:39324470-39344503	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr19:39337391-39338692	A549	lung:	n/a	n/a
7	POLR2A	chr19:39325226-39343915	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:39313168-39344379	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr19:39337355-39338877	GM12892	blood:	n/a	n/a
10	POLR2A	chr19:39337389-39337532	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr19:39337406-39343729	GM12892	blood:	n/a	n/a
12	TCF12	chr19:39337395-39344253	A549	lung:	n/a	chr19:39337932-39337939
13	POLR2A	chr19:39337414-39337564	GM12891	blood:	n/a	n/a
14	POLR2A	chr19:39336355-39337493	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr19:39331012-39342704	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:39337385-39338773	K562	blood:	n/a	n/a
17	POLR2A	chr19:39332839-39343744	K562	blood:	n/a	n/a
18	POLR2A	chr19:39336492-39337495	Hela-S3	cervix:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39217331..39220252-chr19:39336372..39338597,2	K562	blood:
2	chr19:39218752..39222924-chr19:39336082..39338597,4	K562	blood:
3	chr19:39337019..39338579-chr19:39410355..39412359,2	MCF-7	breast:
4	chr19:39212206..39230741-chr19:39336504..39344817,33	MCF-7	breast:
5	chr19:39306785..39309520-chr19:39336164..39339038,3	K562	blood:
6	chr19:39228666..39232672-chr19:39336052..39337743,3	K562	blood:
7	chr19:39310279..39311821-chr19:39336796..39339611,2	K562	blood:
8	chr19:39306612..39310061-chr19:39334754..39339038,4	K562	blood:
9	chr19:39336974..39342883-chr19:39419267..39423173,13	K562	blood:

No data

Variant related genes	Relation type
HNRNPL	TF binding region
ENSG00000269688	TF binding region
ENSG00000267892	Chromatin interaction
ENSG00000104823	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000182472	Chromatin interaction
ENSG00000268756	Chromatin interaction
ENSG00000128626	Chromatin interaction
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10403012	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10411480	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10411844	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10425464	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1078734	0.88[AMR][1000 genomes]
rs11668179	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11668766	0.84[ASN][1000 genomes]
rs11671711	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12974488	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2075587	0.81[AMR][1000 genomes]
rs2075588	0.84[AMR][1000 genomes]
rs2116852	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2278010	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35829996	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4328569	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802928	0.81[EUR][1000 genomes]
rs7248208	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8110679	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs862454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs862457	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs862458	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs862460	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs862461	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs862462	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs862463	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9419	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9789283	0.82[ASN][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	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	esv1792915	chr19:39335274-39341182	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	n/a
4	esv1794032	chr19:39335274-39341182	Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	n/a
5	nsv911673	chr19:39335274-39365401	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12977821	ECH1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39324600-39338000	Strong transcription	Fetal Brain Female	brain
2	chr19:39325400-39337800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:39325400-39337800	Strong transcription	Brain Cingulate Gyrus	brain
4	chr19:39325400-39338000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr19:39325400-39338200	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr19:39325400-39338200	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr19:39325600-39338000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:39326000-39337800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:39326000-39338000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:39326000-39338000	Strong transcription	Brain Anterior Caudate	brain
11	chr19:39326000-39338000	Strong transcription	HSMM	muscle
12	chr19:39326000-39338200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
13	chr19:39326000-39338200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr19:39326000-39338200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr19:39326000-39338200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr19:39326000-39338200	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr19:39326000-39338400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
18	chr19:39326000-39338400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr19:39326000-39338600	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr19:39326200-39337600	Strong transcription	Ovary	ovary
21	chr19:39326200-39337800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:39326200-39337800	Strong transcription	Right Ventricle	heart
23	chr19:39326200-39337800	Strong transcription	HUVEC	blood vessel
24	chr19:39326200-39337800	Strong transcription	K562	blood
25	chr19:39326200-39338000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:39326200-39338000	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr19:39326200-39338200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr19:39326200-39338400	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr19:39326200-39338400	Strong transcription	Fetal Kidney	kidney
30	chr19:39326200-39338800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr19:39326400-39338200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr19:39326400-39338400	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr19:39326600-39337800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr19:39326600-39338200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:39326800-39337800	Strong transcription	NH-A	brain
36	chr19:39326800-39338000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr19:39326800-39338000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr19:39327000-39337800	Strong transcription	Rectal Smooth Muscle	rectum
39	chr19:39327000-39338400	Strong transcription	NHDF-Ad	bronchial
40	chr19:39327600-39337800	Genic enhancers	HepG2	liver
41	chr19:39327600-39338400	Strong transcription	Osteobl	bone
42	chr19:39327800-39338800	Genic enhancers	Liver	Liver
43	chr19:39328000-39338000	Strong transcription	NHLF	lung
44	chr19:39328000-39338400	Strong transcription	Aorta	Aorta
45	chr19:39328600-39338000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr19:39329600-39337800	Weak transcription	Right Atrium	heart
47	chr19:39329800-39337800	Strong transcription	Fetal Lung	lung
48	chr19:39329800-39337800	Strong transcription	Lung	lung
49	chr19:39330400-39337800	Genic enhancers	A549	lung
50	chr19:39330800-39338000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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