Variant report

Variant	rs5997646
Chromosome Location	chr22:30830312-30830313
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30816361..30822733-chr22:30829064..30833429,8	K562	blood:
2	chr22:30785161..30787153-chr22:30828988..30831044,2	MCF-7	breast:
3	chr22:30828166..30830631-chr22:30830647..30834059,3	MCF-7	breast:
4	chr22:30790931..30793617-chr22:30827644..30831113,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000099999	Chromatin interaction
ENSG00000272689	Chromatin interaction
ENSG00000100003	Chromatin interaction
ENSG00000203606	Chromatin interaction
ENSG00000222915	Chromatin interaction
ENSG00000273350	Chromatin interaction
ENSG00000242114	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1005835	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1010324	1.00[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11089442	0.82[CEU][hapmap]
rs11089447	1.00[CEU][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes]
rs11089448	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11089449	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11703867	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11705639	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12171261	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2072160	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2074731	0.91[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs2267154	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2267155	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2267156	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2283870	1.00[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2283871	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2299827	0.91[CEU][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2839998	0.91[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs57940170	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5994294	0.91[CEU][hapmap]
rs5994305	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5994306	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5997637	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61583714	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7288366	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7289360	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7290317	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8141656	0.91[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs9619096	0.91[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs9619105	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9620984	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.95[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	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	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5997646	SYN3	cis	parietal	SCAN
rs5997646	NIPSNAP1	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30822400-30834400	Weak transcription	Small Intestine	intestine
2	chr22:30822600-30831600	Weak transcription	Right Atrium	heart
3	chr22:30822600-30832000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr22:30822800-30831600	Weak transcription	Right Ventricle	heart
5	chr22:30822800-30832000	Weak transcription	Left Ventricle	heart
6	chr22:30823000-30831000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr22:30823000-30831000	Weak transcription	NH-A	brain
8	chr22:30823000-30831200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr22:30823000-30831200	Weak transcription	Fetal Thymus	thymus
10	chr22:30823000-30831600	Weak transcription	Colonic Mucosa	Colon
11	chr22:30823200-30831000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr22:30823200-30831000	Weak transcription	HUVEC	blood vessel
13	chr22:30823200-30831200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr22:30823200-30831600	Weak transcription	Thymus	Thymus
15	chr22:30823200-30831600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr22:30823200-30833600	Weak transcription	Stomach Mucosa	stomach
17	chr22:30823400-30830800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr22:30823600-30830800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr22:30823800-30830600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr22:30824000-30830600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr22:30824400-30831400	Weak transcription	Placenta	Placenta
22	chr22:30824400-30839000	Weak transcription	Hela-S3	cervix
23	chr22:30824600-30831600	Weak transcription	A549	lung
24	chr22:30824800-30831200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr22:30824800-30831200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr22:30824800-30831400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr22:30824800-30834400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr22:30825000-30830800	Weak transcription	K562	blood
29	chr22:30825000-30831200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr22:30825000-30831600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr22:30825000-30831600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr22:30825200-30831000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr22:30825200-30831000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr22:30825200-30831000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr22:30825200-30831400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr22:30825200-30831400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr22:30825200-30831400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr22:30825200-30831600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr22:30825400-30830800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr22:30825400-30830800	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr22:30825400-30831200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr22:30825600-30830800	Weak transcription	GM12878-XiMat	blood
43	chr22:30825600-30831000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr22:30825600-30831200	Weak transcription	Primary T cells from cord blood	blood
45	chr22:30825600-30831200	Weak transcription	Pancreas	Pancrea
46	chr22:30825600-30831600	Weak transcription	Fetal Muscle Leg	muscle
47	chr22:30825600-30831800	Weak transcription	Fetal Stomach	stomach
48	chr22:30825800-30830400	Weak transcription	Dnd41	blood
49	chr22:30826000-30831200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr22:30826400-30831000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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