Variant report

Variant	rs9619096
Chromosome Location	chr22:30696744-30696745
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30692354..30698688-chr22:30699927..30704803,9	K562	blood:

Variant related genes	Relation type
ENSG00000099992	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1010324	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs11089441	1.00[LWK][hapmap]
rs11089442	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11089447	0.91[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs11703385	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11704358	1.00[LWK][hapmap]
rs12169094	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12171261	0.83[EUR][1000 genomes]
rs2074731	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2267154	0.91[CEU][hapmap]
rs2267155	0.91[CEU][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap]
rs2267156	0.91[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs2283866	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283870	0.91[CEU][hapmap]
rs2299827	0.83[CEU][hapmap];0.81[CHB][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs2839998	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57940170	0.83[EUR][1000 genomes]
rs5994294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5994305	0.91[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs5997637	0.91[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs5997646	0.91[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs61583714	0.83[EUR][1000 genomes]
rs71331235	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7288366	0.91[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs7289360	0.83[EUR][1000 genomes]
rs7289384	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7290317	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs8141656	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs929271	1.00[LWK][hapmap]
rs9619098	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9619105	0.83[EUR][1000 genomes]
rs9620984	0.91[CEU][hapmap];0.81[CHB][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv834174	chr22:30619760-30746915	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1062388	chr22:30649179-30711443	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv1799458	chr22:30659798-30698035	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9619096	SYN3	cis	parietal	SCAN
rs9619096	TTC28AS	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30686000-30700000	Weak transcription	Fetal Kidney	kidney
2	chr22:30686200-30720000	Weak transcription	Fetal Brain Male	brain
3	chr22:30686400-30701800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr22:30686600-30700600	Genic enhancers	Fetal Thymus	thymus
5	chr22:30686800-30701800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr22:30686800-30707200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr22:30687000-30699600	Strong transcription	Fetal Brain Female	brain
8	chr22:30687200-30697200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr22:30687400-30701200	Weak transcription	K562	blood
10	chr22:30687400-30706800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr22:30687600-30697200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr22:30687600-30699000	Weak transcription	HepG2	liver
13	chr22:30687600-30699800	Genic enhancers	Esophagus	oesophagus
14	chr22:30687600-30701400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr22:30687800-30697600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr22:30687800-30698000	Strong transcription	Osteobl	bone
17	chr22:30688000-30697400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr22:30688000-30697400	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr22:30688000-30697600	Weak transcription	HUVEC	blood vessel
20	chr22:30688200-30696800	Strong transcription	Duodenum Mucosa	Duodenum
21	chr22:30688200-30697200	Weak transcription	Brain Angular Gyrus	brain
22	chr22:30688200-30697200	Strong transcription	HSMMtube	muscle
23	chr22:30688200-30697800	Strong transcription	NHLF	lung
24	chr22:30688200-30698400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr22:30688200-30698600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr22:30688200-30699200	Strong transcription	Aorta	Aorta
27	chr22:30688200-30700600	Strong transcription	Fetal Stomach	stomach
28	chr22:30688400-30696800	Strong transcription	Fetal Muscle Leg	muscle
29	chr22:30688400-30697400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr22:30688400-30697800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr22:30688400-30697800	Strong transcription	Liver	Liver
32	chr22:30688400-30698000	Strong transcription	GM12878-XiMat	blood
33	chr22:30688600-30697800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr22:30689800-30698200	Weak transcription	A549	lung
35	chr22:30690200-30699000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr22:30690200-30700200	Genic enhancers	Primary T cells fromperipheralblood	blood
37	chr22:30690400-30698000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
38	chr22:30690400-30700800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr22:30690800-30699800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr22:30690800-30701600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr22:30691000-30697800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr22:30691000-30706800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr22:30691400-30697200	Strong transcription	HSMM	muscle
44	chr22:30692000-30697600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr22:30692000-30697600	Strong transcription	Fetal Muscle Trunk	muscle
46	chr22:30692600-30697000	Weak transcription	Brain Substantia Nigra	brain
47	chr22:30692600-30697800	Weak transcription	Small Intestine	intestine
48	chr22:30692800-30700600	Genic enhancers	Placenta	Placenta
49	chr22:30693200-30701000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr22:30693400-30697000	Strong transcription	Muscle Satellite Cultured Cells	--

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