Variant report

Variant	rs10401588
Chromosome Location	chr19:51305287-51305288
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:51305171-51308575	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr19:51305218-51308754	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr19:51305245-51305784	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:51305213-51308097	GM12892	blood:	n/a	n/a
5	POLR2A	chr19:51305153-51308634	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:51305233-51305655	GM12891	blood:	n/a	n/a
7	POLR2A	chr19:51305170-51308571	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr19:51305179-51309471	HepG2	liver:	n/a	n/a
9	POLR2A	chr19:51305174-51308584	GM12892	blood:	n/a	n/a
10	HEY1	chr19:51305231-51308447	K562	blood:	n/a	chr19:51307531-51307546
11	POLR2A	chr19:51305284-51305679	HepG2	liver:	n/a	n/a
12	POLR2A	chr19:51305232-51306290	K562	blood:	n/a	n/a
13	POLR2A	chr19:51305176-51308591	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:51305256-51305842	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr19:51305263-51307426	GM12891	blood:	n/a	n/a
16	POLR2A	chr19:51305034-51308640	GM12892	blood:	n/a	n/a
17	POLR2A	chr19:51305200-51308131	GM12891	blood:	n/a	n/a
18	POLR2A	chr19:51305261-51305836	GM12892	blood:	n/a	n/a
19	POLR2A	chr19:51305272-51308541	K562	blood:	n/a	n/a
20	POLR2A	chr19:51305191-51305880	PFSK-1	brain:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:51303704..51306185-chr19:51373080..51375734,4	K562	blood:
2	chr19:51304876..51308314-chr19:51372660..51375800,4	MCF-7	breast:
3	chr19:51225811..51229710-chr19:51304326..51309315,7	K562	blood:
4	chr19:51303704..51305752-chr19:51372094..51375734,4	K562	blood:

No data

Variant related genes	Relation type
SNORD88A	TF binding region
SNORD88B	TF binding region
ENSG00000105472	Chromatin interaction
ENSG00000167751	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1043315	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11668685	0.88[ASN][1000 genomes]
rs11668998	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12610777	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3745526	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3745528	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3865442	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4801853	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802741	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802742	0.88[ASN][1000 genomes]
rs55735528	0.86[AMR][1000 genomes]
rs55929248	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7258708	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9991	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][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	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv912288	chr19:51283791-51334355	Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
4	nsv912289	chr19:51283791-51335943	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
5	nsv912290	chr19:51283791-51344483	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
6	nsv526232	chr19:51301230-51335943	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
7	esv3359731	chr19:51305056-51305299	Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10401588	C19orf48	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51297000-51306200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr19:51297800-51305600	Weak transcription	Fetal Brain Male	brain
3	chr19:51297800-51306200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr19:51298000-51305400	Weak transcription	Fetal Heart	heart
5	chr19:51298200-51305400	Strong transcription	Fetal Intestine Small	intestine
6	chr19:51298200-51305400	Strong transcription	Fetal Stomach	stomach
7	chr19:51298200-51305800	Strong transcription	Brain Germinal Matrix	brain
8	chr19:51298200-51306000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr19:51298200-51306800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr19:51298400-51305400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr19:51298400-51305400	Strong transcription	Fetal Muscle Leg	muscle
12	chr19:51298400-51305800	Strong transcription	Skeletal Muscle Male	skeletal muscle
13	chr19:51298600-51305400	Strong transcription	H9 Cell Line	embryonic stem cell
14	chr19:51298600-51305400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr19:51298600-51305400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr19:51298600-51305400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr19:51298600-51305600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:51298600-51305600	Strong transcription	Fetal Brain Female	brain
19	chr19:51298800-51305400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:51298800-51305400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:51298800-51305400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr19:51298800-51305600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr19:51299000-51305400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr19:51299000-51305400	Strong transcription	Liver	Liver
25	chr19:51299200-51305800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr19:51299400-51305400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:51299400-51305600	Weak transcription	NHDF-Ad	bronchial
28	chr19:51299400-51305800	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr19:51299600-51305400	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr19:51299600-51305400	Strong transcription	NHEK	skin
31	chr19:51299600-51305800	Strong transcription	Lung	lung
32	chr19:51299800-51305600	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr19:51299800-51305600	Strong transcription	Placenta	Placenta
34	chr19:51300000-51305400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:51300000-51305600	Strong transcription	Fetal Thymus	thymus
36	chr19:51300000-51305800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr19:51300000-51306800	Weak transcription	Right Atrium	heart
38	chr19:51300200-51305400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr19:51300200-51305400	Strong transcription	Fetal Intestine Large	intestine
40	chr19:51300200-51305600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:51300200-51305800	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr19:51300400-51305400	Strong transcription	Fetal Lung	lung
43	chr19:51300400-51305800	Strong transcription	Ovary	ovary
44	chr19:51300600-51305400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
45	chr19:51300800-51305400	Strong transcription	HUVEC	blood vessel
46	chr19:51300800-51306200	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr19:51301000-51305400	Strong transcription	NHLF	lung
48	chr19:51301000-51305800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
49	chr19:51301200-51305800	Strong transcription	Osteobl	bone
50	chr19:51301400-51305400	Genic enhancers	A549	lung

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