Variant report

Variant	rs9613560
Chromosome Location	chr22:28404167-28404168
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	chr22:28401032..28403259-chr22:28403789..28405576,2	K562	blood:
2	chr22:28393472..28395855-chr22:28403235..28405878,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HSCB-1	chr22:28402517-28404569	ENSG00000235954

Variant related genes	Relation type
ENSG00000235954	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11090520	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17409164	1.00[AFR][1000 genomes]
rs17409195	1.00[AFR][1000 genomes]
rs17480516	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17483415	0.88[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs738398	1.00[AFR][1000 genomes]
rs738455	0.90[EUR][1000 genomes]
rs738474	0.88[CEU][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9608663	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9608665	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs9608666	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9608672	1.00[AFR][1000 genomes]
rs9613549	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9613552	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9613558	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9613564	0.86[EUR][1000 genomes]
rs9613568	0.88[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs9613569	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9613573	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9613560	HPS4	cis	parietal	SCAN
rs9613560	CRYBB2P1	cis	parietal	SCAN
rs9613560	SF3A1	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28373800-28404200	Strong transcription	Fetal Stomach	stomach
2	chr22:28373800-28405200	Strong transcription	Fetal Intestine Small	intestine
3	chr22:28381800-28412400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr22:28384000-28405000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr22:28386200-28405800	Strong transcription	Dnd41	blood
6	chr22:28386200-28416000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr22:28387400-28405200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr22:28387600-28405000	Weak transcription	Fetal Kidney	kidney
9	chr22:28389200-28410000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr22:28389200-28413000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr22:28390000-28414600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr22:28390400-28416200	Weak transcription	Colonic Mucosa	Colon
13	chr22:28392200-28405200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr22:28393400-28408800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr22:28394200-28405000	Weak transcription	Fetal Brain Male	brain
16	chr22:28394200-28405000	Weak transcription	NHDF-Ad	bronchial
17	chr22:28394800-28414000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr22:28395000-28416400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr22:28395200-28405000	Weak transcription	Brain Substantia Nigra	brain
20	chr22:28395200-28405200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr22:28395200-28409200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr22:28395400-28404600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr22:28395400-28406400	Weak transcription	Aorta	Aorta
24	chr22:28395400-28409200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr22:28395600-28408200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr22:28395600-28413000	Weak transcription	Pancreas	Pancrea
27	chr22:28396000-28422400	Weak transcription	Primary T cells from cord blood	blood
28	chr22:28396800-28407600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr22:28397200-28404200	Weak transcription	Colon Smooth Muscle	Colon
30	chr22:28397200-28405000	Weak transcription	Brain Hippocampus Middle	brain
31	chr22:28397200-28409400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr22:28397200-28423000	Weak transcription	HepG2	liver
33	chr22:28397400-28405000	Weak transcription	Brain Anterior Caudate	brain
34	chr22:28397400-28408800	Weak transcription	Brain Angular Gyrus	brain
35	chr22:28397400-28412000	Weak transcription	Placenta	Placenta
36	chr22:28397600-28404600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr22:28397600-28405000	Weak transcription	Gastric	stomach
38	chr22:28398000-28405200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr22:28398400-28405600	Weak transcription	Esophagus	oesophagus
40	chr22:28399400-28425800	Weak transcription	Liver	Liver
41	chr22:28399600-28409000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr22:28400600-28405200	Weak transcription	Fetal Intestine Large	intestine
43	chr22:28400800-28410200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr22:28401600-28404600	Weak transcription	Ovary	ovary
45	chr22:28401600-28405000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr22:28401600-28405200	Weak transcription	Adipose Nuclei	Adipose
47	chr22:28401600-28405200	Weak transcription	Fetal Lung	lung
48	chr22:28401600-28409000	Strong transcription	Fetal Muscle Leg	muscle
49	chr22:28401600-28412000	Weak transcription	Thymus	Thymus
50	chr22:28401800-28407800	Weak transcription	Lung	lung

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