Variant report

Variant	rs5762399
Chromosome Location	chr22:28306607-28306608
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28305823..28310839-chr22:28313322..28318569,8	MCF-7	breast:
2	chr22:28303429..28305158-chr22:28305808..28308439,2	K562	blood:

Variant related genes	Relation type
ENSG00000180957	Chromatin interaction
ENSG00000235954	Chromatin interaction
ENSG00000264073	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1016495	0.84[CEU][hapmap]
rs7287702	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs7292046	0.84[CEU][hapmap]
rs738454	0.84[CEU][hapmap]

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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv588878	chr22:28248840-28314113	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5762399	TTC28AS	cis	cerebellum	SCAN
rs5762399	CYTSA	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28247000-28311800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:28277200-28308600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr22:28277800-28308400	Strong transcription	Dnd41	blood
4	chr22:28280600-28308000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr22:28281600-28308000	Strong transcription	Fetal Muscle Trunk	muscle
6	chr22:28283000-28307000	Strong transcription	Fetal Intestine Large	intestine
7	chr22:28283200-28307600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr22:28283600-28310000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr22:28283800-28308000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr22:28286000-28309000	Weak transcription	Stomach Mucosa	stomach
11	chr22:28286200-28311400	Weak transcription	Right Atrium	heart
12	chr22:28288600-28309400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr22:28289000-28312600	Weak transcription	Psoas Muscle	Psoas
14	chr22:28292600-28307800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr22:28292800-28307200	Strong transcription	Liver	Liver
16	chr22:28292800-28309200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr22:28293200-28309000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr22:28293800-28309200	Weak transcription	Brain Substantia Nigra	brain
19	chr22:28293800-28309600	Weak transcription	Right Ventricle	heart
20	chr22:28293800-28311800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr22:28294000-28309200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr22:28295200-28309200	Weak transcription	Brain Angular Gyrus	brain
23	chr22:28295200-28313800	Weak transcription	Colonic Mucosa	Colon
24	chr22:28296200-28308200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr22:28297000-28307200	Strong transcription	Fetal Lung	lung
26	chr22:28298200-28307800	Strong transcription	HSMM	muscle
27	chr22:28298400-28314000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr22:28299200-28314000	Weak transcription	Spleen	Spleen
29	chr22:28299400-28310200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr22:28299800-28307000	Strong transcription	A549	lung
31	chr22:28300000-28307600	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr22:28300000-28308000	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr22:28300200-28307000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr22:28300200-28308000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr22:28300400-28307600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr22:28300400-28308000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr22:28300400-28308000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr22:28300400-28309200	Weak transcription	Small Intestine	intestine
39	chr22:28300400-28311400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr22:28300600-28308400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr22:28300800-28306800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr22:28300800-28309200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr22:28301000-28307600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr22:28301000-28307800	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr22:28301200-28307400	Strong transcription	GM12878-XiMat	blood
46	chr22:28301200-28307400	Strong transcription	K562	blood
47	chr22:28301400-28307200	Strong transcription	HUVEC	blood vessel
48	chr22:28301400-28309800	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr22:28301600-28307400	Strong transcription	NH-A	brain
50	chr22:28301600-28308200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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