Variant report

Variant	rs10403322
Chromosome Location	chr19:19145598-19145599
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr19:19142926-19145719	SK-N-SH	brain:	n/a	chr19:19144717-19144726 chr19:19144719-19144728 chr19:19144719-19144728
2	SIN3AK20	chr19:19144106-19145622	MCF-7	breast:	n/a	n/a
3	POLR2A	chr19:19144085-19145617	PFSK-1	brain:	n/a	n/a
4	MAX	chr19:19143612-19145663	K562	blood:	n/a	chr19:19144718-19144727 chr19:19144718-19144727 chr19:19144718-19144727 chr19:19144718-19144728
5	POLR2A	chr19:19144080-19145622	SK-N-MC	brain:	n/a	n/a
6	MYC	chr19:19144223-19145693	A549	lung:	n/a	chr19:19144718-19144727 chr19:19144718-19144727 chr19:19144718-19144727 chr19:19144718-19144728
7	SIN3AK20	chr19:19144339-19145598	MCF-7	breast:	n/a	n/a
8	MXI1	chr19:19142682-19145691	IMR90	lung:	n/a	chr19:19144717-19144726 chr19:19144719-19144728 chr19:19144719-19144728

No.	Distal block	Cell Line	Cell type
1	chr19:19141992..19145825-chr19:19171077..19177701,15	K562	blood:
2	chr19:19143660..19145632-chr19:19301840..19304072,2	MCF-7	breast:
3	chr19:19143657..19146284-chr19:19174594..19176382,2	MCF-7	breast:
4	chr19:19141992..19145925-chr19:19172787..19177854,10	K562	blood:
5	chr19:19028019..19031021-chr19:19142402..19146031,5	K562	blood:

Variant related genes	Relation type
SUGP2	TF binding region
ENSG00000181035	Chromatin interaction
ENSG00000105669	Chromatin interaction
ENSG00000105671	Chromatin interaction
ENSG00000254901	Chromatin interaction
ENSG00000064490	Chromatin interaction
ENSG00000213999	Chromatin interaction
ENSG00000064489	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10403222	0.84[EUR][1000 genomes]
rs10423815	0.82[EUR][1000 genomes]
rs10854005	0.84[EUR][1000 genomes]
rs11666340	0.83[EUR][1000 genomes]
rs11670204	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11670239	0.82[EUR][1000 genomes]
rs12979565	0.85[EUR][1000 genomes]
rs2107263	0.84[EUR][1000 genomes]
rs2240095	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2872394	0.83[EUR][1000 genomes]
rs4808907	0.84[EUR][1000 genomes]
rs4808913	0.84[EUR][1000 genomes]
rs6511010	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6511011	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6511014	0.84[EUR][1000 genomes]
rs7258637	0.83[EUR][1000 genomes]
rs8101529	0.84[EUR][1000 genomes]
rs8104799	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8106146	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8109654	0.85[EUR][1000 genomes]
rs8110629	0.84[EUR][1000 genomes]
rs8112566	0.86[EUR][1000 genomes]
rs916898	0.82[EUR][1000 genomes]
rs929215	0.83[EUR][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	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv1059305	chr19:19131310-19209999	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
3	esv3362167	chr19:19143102-19145750	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10403322	TMEM161A	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19143000-19145600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr19:19143000-19145600	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr19:19143000-19145600	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr19:19143000-19145600	Active TSS	GM12878-XiMat	blood
5	chr19:19143000-19145600	Active TSS	HSMM	muscle
6	chr19:19143000-19145600	Active TSS	NHDF-Ad	bronchial
7	chr19:19143000-19145600	Active TSS	NHLF	lung
8	chr19:19143000-19146000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:19143200-19145600	Active TSS	H9 Cell Line	embryonic stem cell
10	chr19:19143200-19145600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:19143200-19145600	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr19:19143200-19145600	Active TSS	Fetal Kidney	kidney
13	chr19:19143200-19145600	Active TSS	HSMMtube	muscle
14	chr19:19143400-19146000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr19:19143600-19145600	Active TSS	Fetal Brain Female	brain
16	chr19:19144600-19145600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr19:19144600-19145600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr19:19144600-19145600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr19:19144600-19145600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:19144600-19145800	Flanking Active TSS	Dnd41	blood
21	chr19:19144800-19145600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr19:19144800-19145600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:19144800-19145600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:19144800-19145600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:19144800-19145600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr19:19144800-19145600	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr19:19144800-19145600	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr19:19144800-19145600	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr19:19144800-19145600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr19:19144800-19145600	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr19:19144800-19145600	Flanking Active TSS	Placenta	Placenta
32	chr19:19144800-19145600	Flanking Active TSS	Fetal Thymus	thymus
33	chr19:19144800-19145600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr19:19144800-19145600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr19:19144800-19145600	Flanking Active TSS	Right Ventricle	heart
36	chr19:19144800-19145600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr19:19144800-19145600	Flanking Active TSS	Hela-S3	cervix
38	chr19:19144800-19145600	Flanking Active TSS	HMEC	breast
39	chr19:19144800-19145600	Flanking Active TSS	HUVEC	blood vessel
40	chr19:19144800-19145600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr19:19145000-19145600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr19:19145000-19145600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr19:19145000-19145600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr19:19145000-19145600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr19:19145000-19145600	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr19:19145000-19145600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr19:19145000-19145600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr19:19145000-19145600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr19:19145000-19145600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr19:19145000-19145600	Flanking Active TSS	Brain Angular Gyrus	brain

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