Variant report

Variant	rs10424229
Chromosome Location	chr19:18641582-18641583
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:18641232-18641623	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18638375..18642059-chr19:18698686..18701934,3	K562	blood:
2	chr19:18625885..18628372-chr19:18639821..18642383,2	MCF-7	breast:
3	chr19:18631013..18633168-chr19:18641014..18643926,2	MCF-7	breast:
4	chr19:18640795..18642364-chr19:18950530..18953348,2	K562	blood:
5	chr19:18632022..18634941-chr19:18640789..18642587,3	K562	blood:
6	chr19:18640357..18642464-chr19:18650908..18653787,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000268938	TF binding region
ENSG00000269191	TF binding region
ENSG00000105701	Chromatin interaction
ENSG00000006015	Chromatin interaction
ENSG00000105656	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10401741	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10415320	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10422974	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11086113	0.85[EUR][1000 genomes]
rs12986175	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs983141	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv428018	chr19:18454891-18663981	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
5	nsv1060687	chr19:18522527-18643218	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
7	nsv1061733	chr19:18574940-18679155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	nsv1055794	chr19:18611545-18676933	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
10	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
11	nsv911283	chr19:18626732-18689830	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
12	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10424229	SSBP4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18632800-18642200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:18632800-18642200	Weak transcription	Aorta	Aorta
3	chr19:18632800-18652200	Weak transcription	Fetal Heart	heart
4	chr19:18632800-18652800	Weak transcription	Stomach Mucosa	stomach
5	chr19:18632800-18654600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr19:18633000-18642000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:18633000-18642000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr19:18633000-18642000	Weak transcription	Lung	lung
9	chr19:18633000-18642200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr19:18633000-18642200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr19:18633000-18642200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr19:18633000-18642200	Weak transcription	Liver	Liver
13	chr19:18633000-18642200	Weak transcription	Colonic Mucosa	Colon
14	chr19:18633000-18642200	Weak transcription	Esophagus	oesophagus
15	chr19:18633000-18642200	Weak transcription	Gastric	stomach
16	chr19:18633000-18642200	Weak transcription	Left Ventricle	heart
17	chr19:18633000-18642200	Weak transcription	Pancreas	Pancrea
18	chr19:18633000-18642200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr19:18633000-18642200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr19:18633000-18642800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr19:18633000-18653400	Weak transcription	Psoas Muscle	Psoas
22	chr19:18633200-18653200	Weak transcription	Right Atrium	heart
23	chr19:18633600-18642200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr19:18633600-18642200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr19:18633600-18642200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr19:18633600-18642200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr19:18633600-18642200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr19:18633600-18642200	Weak transcription	HSMMtube	muscle
29	chr19:18633600-18642200	Weak transcription	NHLF	lung
30	chr19:18633600-18645200	Weak transcription	HSMM	muscle
31	chr19:18633600-18646600	Weak transcription	Small Intestine	intestine
32	chr19:18633800-18641800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr19:18633800-18641800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr19:18633800-18642000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr19:18633800-18642000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr19:18633800-18642000	Weak transcription	Adipose Nuclei	Adipose
37	chr19:18633800-18642000	Weak transcription	Brain Hippocampus Middle	brain
38	chr19:18633800-18642000	Weak transcription	Fetal Brain Female	brain
39	chr19:18633800-18642000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr19:18633800-18642000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr19:18633800-18642000	Weak transcription	Osteobl	bone
42	chr19:18633800-18642200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr19:18633800-18642200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:18633800-18642200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr19:18633800-18642200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr19:18633800-18642200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr19:18633800-18642200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr19:18633800-18642200	Weak transcription	Primary B cells from cord blood	blood
49	chr19:18633800-18642200	Weak transcription	Primary T cells from cord blood	blood
50	chr19:18633800-18642200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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