Variant report

Variant	rs2411321
Chromosome Location	chr19:51896929-51896930
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr19:51896896-51898500	SK-N-SH	brain:	n/a	n/a
2	GTF3C2	chr19:51896816-51897595	K562	blood:	n/a	n/a
3	POLR2A	chr19:51896843-51899037	K562	blood:	n/a	n/a
4	TCF12	chr19:51896852-51898436	A549	lung:	n/a	chr19:51898333-51898343
5	ZC3H11A	chr19:51896728-51898299	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:51852221..51854655-chr19:51896063..51897608,2	K562	blood:
2	chr19:51895053..51897765-chr19:52007493..52009642,2	K562	blood:
3	chr19:51840838..51845657-chr19:51892354..51900411,18	K562	blood:
4	chr19:51896400..51903695-chr19:51903717..51912186,11	K562	blood:
5	chr19:51894435..51896093-chr19:51896097..51897636,2	K562	blood:
6	chr19:51841257..51845442-chr19:51896216..51899567,12	K562	blood:
7	chr19:51896384..51897937-chr19:51904154..51907057,2	MCF-7	breast:
8	chr19:51867772..51875803-chr19:51892381..51899756,21	K562	blood:
9	chr19:51864453..51872845-chr19:51892428..51902096,29	K562	blood:
10	chr19:51889349..51894566-chr19:51895156..51899826,6	K562	blood:
11	chr19:51889722..51893942-chr19:51894149..51900029,8	K562	blood:

No data

Variant related genes	Relation type
C19orf84	TF binding region
ENSG00000268889	TF binding region
ENSG00000267905	Chromatin interaction
ENSG00000105374	Chromatin interaction
ENSG00000269403	Chromatin interaction
ENSG00000268144	Chromatin interaction
ENSG00000268520	Chromatin interaction
ENSG00000105379	Chromatin interaction
ENSG00000105370	Chromatin interaction
ENSG00000160318	Chromatin interaction
ENSG00000186806	Chromatin interaction
ENSG00000268839	Chromatin interaction
ENSG00000262874	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10403762	0.87[ASN][1000 genomes]
rs10404198	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10419880	0.91[ASN][1000 genomes]
rs11084075	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11084076	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11084077	0.92[ASN][1000 genomes]
rs11669975	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11670065	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11673263	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2411322	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2547308	0.86[ASN][1000 genomes]
rs2547309	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2741240	0.82[ASN][1000 genomes]
rs2741241	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3810093	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3810094	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3810095	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3810096	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3810097	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3826657	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3826658	0.87[ASN][1000 genomes]
rs3826659	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3826660	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3826663	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3826664	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3826665	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4377257	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4441376	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7250926	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7251238	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7251286	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7251311	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7251566	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7257275	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7508570	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8100861	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8104425	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8107533	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8111906	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2411321	CTD-2616J11.4	cis	Whole Blood	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51872000-51897000	Weak transcription	Right Atrium	heart
2	chr19:51889200-51897000	Weak transcription	Spleen	Spleen
3	chr19:51891000-51897000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr19:51891600-51897000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:51891800-51897000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:51891800-51897000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:51891800-51897000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:51892600-51897000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr19:51894200-51897000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr19:51894200-51897000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr19:51894200-51897000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr19:51894200-51897000	Weak transcription	Placenta	Placenta
13	chr19:51894200-51897000	Weak transcription	Fetal Stomach	stomach
14	chr19:51894400-51897000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr19:51894400-51897000	Weak transcription	Primary T cells from cord blood	blood
16	chr19:51894400-51897000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr19:51894400-51897000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr19:51894400-51897000	Weak transcription	Fetal Muscle Leg	muscle
19	chr19:51894400-51897000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr19:51894400-51897000	Weak transcription	NHDF-Ad	bronchial
21	chr19:51894400-51897000	Weak transcription	Osteobl	bone
22	chr19:51894400-51897200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr19:51894600-51897000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr19:51894600-51897000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr19:51894600-51897000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr19:51894600-51897000	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr19:51894600-51897000	Weak transcription	Primary B cells from cord blood	blood
28	chr19:51894600-51897000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr19:51894600-51897000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr19:51894600-51897000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr19:51894600-51897000	Weak transcription	Esophagus	oesophagus
32	chr19:51894600-51897000	Weak transcription	Fetal Lung	lung
33	chr19:51894600-51897000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr19:51894600-51897000	Weak transcription	Thymus	Thymus
35	chr19:51894800-51897000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr19:51894800-51897000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr19:51894800-51897000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr19:51894800-51897000	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr19:51894800-51897000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr19:51894800-51897000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr19:51894800-51897000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr19:51894800-51897000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr19:51894800-51897000	Weak transcription	Fetal Intestine Large	intestine
44	chr19:51894800-51897000	Weak transcription	Fetal Intestine Small	intestine
45	chr19:51894800-51897000	Weak transcription	HepG2	liver
46	chr19:51894800-51897000	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr19:51895000-51897000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr19:51895000-51897000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:51895000-51897000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:51895000-51897000	Weak transcription	Duodenum Mucosa	Duodenum

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