Variant report

Variant	rs17779789
Chromosome Location	chr22:33347576-33347577
allele	C/T
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	GATA3	chr22:33347182-33347794	SH-SY5Y	brain:	n/a	chr22:33347597-33347607 chr22:33347590-33347611 chr22:33347597-33347604 chr22:33347597-33347604 chr22:33347595-33347604 chr22:33347597-33347604
2	YY1	chr22:33347020-33347576	H1-hESC	embryonic stem cell:	n/a	chr22:33347277-33347289
3	GATA2	chr22:33347202-33348054	SH-SY5Y	brain:	n/a	chr22:33347597-33347607 chr22:33347590-33347611 chr22:33347597-33347604 chr22:33347597-33347604 chr22:33347595-33347604 chr22:33347597-33347604
4	EP300	chr22:33347097-33348431	SK-N-SH	brain:	n/a	n/a
5	MXI1	chr22:33346885-33348275	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	22:32846948-32860159..22:33339333-33353583	K562	blood:
2	chr22:32924702..32925549-chr22:33347301..33347897,2	K562	blood:

Variant related genes	Relation type
SYN3	TF binding region
ENSG00000185666	Chromatin interaction
ENSG00000184459	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10483168	1.00[JPT][hapmap]
rs11089599	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11703516	0.83[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11703670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11703699	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11703817	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11703888	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11704480	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11704652	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11704744	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11704887	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11704993	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12158631	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs133928	1.00[CHB][hapmap];0.83[MEX][hapmap]
rs137543	1.00[CHB][hapmap]
rs137559	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs137560	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs137561	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs137564	0.88[AMR][1000 genomes]
rs1991375	1.00[ASW][hapmap];0.81[CEU][hapmap]
rs2042793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2042794	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081727	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs25112	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35463351	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4441575	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5994648	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5994649	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5994652	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5994654	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs5998668	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998681	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998682	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998689	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5998693	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs5998697	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73158385	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73158393	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73162010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73162024	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73162026	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73162029	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73162032	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8139118	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8139584	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8142585	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	nsv531568	chr22:33336868-33480272	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv531587	chr22:33346710-33809338	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17779789	GAL3ST1	cis	cerebellum	SCAN
rs17779789	MTMR3	cis	parietal	SCAN
rs17779789	LIF	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33314000-33380800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr22:33341600-33349600	Weak transcription	Fetal Brain Male	brain
3	chr22:33343200-33372600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr22:33343600-33353000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr22:33344200-33360400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr22:33345000-33349200	Enhancers	Fetal Heart	heart
7	chr22:33345000-33350800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr22:33345200-33348200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr22:33345200-33348400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr22:33345400-33348400	Enhancers	Fetal Muscle Leg	muscle
11	chr22:33345400-33348600	Enhancers	Placenta	Placenta
12	chr22:33345400-33348600	Enhancers	Left Ventricle	heart
13	chr22:33345600-33348400	Enhancers	Fetal Lung	lung
14	chr22:33345600-33348600	Enhancers	Right Atrium	heart
15	chr22:33345800-33347600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr22:33345800-33347800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr22:33345800-33348200	Enhancers	Right Ventricle	heart
18	chr22:33345800-33348200	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr22:33345800-33349000	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr22:33346000-33348400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr22:33346000-33348400	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr22:33346000-33349000	Enhancers	Fetal Stomach	stomach
23	chr22:33346200-33347800	Enhancers	Adipose Nuclei	Adipose
24	chr22:33346200-33348200	Enhancers	Brain Substantia Nigra	brain
25	chr22:33346200-33348200	Enhancers	NHDF-Ad	bronchial
26	chr22:33346200-33348400	Enhancers	Primary hematopoietic stem cells	blood
27	chr22:33346400-33347600	Weak transcription	HSMMtube	muscle
28	chr22:33346400-33348200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr22:33346400-33348200	Enhancers	Placenta Amnion	Placenta Amnion
30	chr22:33346600-33347800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr22:33346600-33348000	Enhancers	Psoas Muscle	Psoas
32	chr22:33346600-33348200	Enhancers	Colon Smooth Muscle	Colon
33	chr22:33346600-33348200	Enhancers	Duodenum Mucosa	Duodenum
34	chr22:33346800-33347800	Enhancers	Brain Anterior Caudate	brain
35	chr22:33346800-33348200	Enhancers	Brain Hippocampus Middle	brain
36	chr22:33346800-33348200	Enhancers	Rectal Smooth Muscle	rectum
37	chr22:33346800-33348200	Enhancers	Stomach Smooth Muscle	stomach
38	chr22:33347000-33347800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
39	chr22:33347000-33348200	Enhancers	Spleen	Spleen
40	chr22:33347200-33347600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr22:33347200-33347600	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr22:33347200-33347800	Enhancers	Ovary	ovary
43	chr22:33347200-33347800	Enhancers	Small Intestine	intestine
44	chr22:33347200-33348000	Enhancers	Lung	lung
45	chr22:33347200-33348200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr22:33347200-33348800	Enhancers	Fetal Muscle Trunk	muscle
47	chr22:33347400-33347600	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr22:33347400-33347600	Enhancers	Fetal Intestine Small	intestine
49	chr22:33347400-33348200	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr22:33347400-33348200	Enhancers	Fetal Kidney	kidney

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