Variant report

Variant	rs822490
Chromosome Location	chr1:155822971-155822972
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155821549..155823556-chr1:155827690..155829206,2	K562	blood:
2	chr1:155821775..155825361-chr1:155825507..155828654,6	MCF-7	breast:
3	chr1:155656761..155658571-chr1:155822378..155824933,2	K562	blood:

Variant related genes	Relation type
ENSG00000116580	Chromatin interaction
ENSG00000163374	Chromatin interaction
ENSG00000132676	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10908479	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs10908481	0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs12035524	0.80[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap]
rs12047756	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs12563627	0.80[JPT][hapmap];0.83[MEX][hapmap]
rs12744132	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1749405	0.80[JPT][hapmap];0.82[MEX][hapmap]
rs1749410	0.84[EUR][1000 genomes]
rs2175391	0.95[CHD][hapmap];0.82[JPT][hapmap]
rs2993207	0.80[JPT][hapmap];0.83[MEX][hapmap]
rs348196	0.80[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap]
rs3738590	0.95[CHD][hapmap];0.82[JPT][hapmap]
rs3820594	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs4661151	0.83[MEX][hapmap]
rs4661175	0.87[MEX][hapmap]
rs475550	0.95[CHD][hapmap];0.82[JPT][hapmap]
rs488079	0.80[JPT][hapmap];0.82[MEX][hapmap]
rs625658	0.80[JPT][hapmap];0.83[MEX][hapmap]
rs6427286	0.90[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs644853	0.93[YRI][hapmap]
rs670876	0.80[CHB][hapmap]
rs678157	0.82[JPT][hapmap]
rs708611	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap]
rs729022	0.85[CEU][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs7517204	0.84[EUR][1000 genomes]
rs7541060	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs7556519	1.00[ASN][1000 genomes]
rs821551	0.92[CEU][hapmap];0.84[CHB][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs822478	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs822494	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs822505	0.84[CEU][hapmap];0.80[JPT][hapmap];0.83[EUR][1000 genomes]
rs822508	0.85[CEU][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs822509	0.83[EUR][1000 genomes]
rs860295	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1003170	chr1:155762204-155836564	Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs822490	YY1AP1	cis	cerebellum	SCAN
rs822490	ADAM15	cis	multi-tissue	Pritchard
rs822490	RIT1	cis	cerebellum	SCAN
rs822490	PRUNE	cis	cerebellum	SCAN
rs822490	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs822490	SPRR3	cis	parietal	SCAN
rs822490	BCAN	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155783600-155823000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:155792200-155826000	Weak transcription	Stomach Mucosa	stomach
3	chr1:155792400-155826600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:155803800-155826000	Weak transcription	Right Atrium	heart
5	chr1:155808000-155826000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:155810000-155825200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr1:155810400-155825400	Strong transcription	Fetal Stomach	stomach
8	chr1:155810600-155825400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr1:155811400-155825000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:155812400-155825400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:155812800-155825400	Strong transcription	Fetal Thymus	thymus
12	chr1:155813000-155825400	Strong transcription	Thymus	Thymus
13	chr1:155813200-155826200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:155813600-155826200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:155813800-155826000	Weak transcription	Right Ventricle	heart
16	chr1:155815200-155825400	Strong transcription	Fetal Intestine Small	intestine
17	chr1:155815200-155825800	Weak transcription	Fetal Heart	heart
18	chr1:155815800-155823000	Weak transcription	HSMMtube	muscle
19	chr1:155815800-155826000	Weak transcription	Psoas Muscle	Psoas
20	chr1:155817200-155825400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:155817200-155825600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:155817400-155823200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
23	chr1:155818200-155825200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr1:155818400-155825000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:155819000-155824400	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr1:155819400-155825400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:155819400-155825400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:155819400-155825600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:155819600-155824600	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr1:155819600-155825400	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:155819600-155825400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:155819800-155823600	Strong transcription	Brain Angular Gyrus	brain
33	chr1:155819800-155823600	Genic enhancers	Dnd41	blood
34	chr1:155819800-155824800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:155819800-155825000	Strong transcription	Osteobl	bone
36	chr1:155819800-155825400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:155819800-155825400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:155819800-155825400	Strong transcription	Liver	Liver
39	chr1:155819800-155825600	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:155820000-155824600	Strong transcription	Fetal Intestine Large	intestine
41	chr1:155820000-155824800	Strong transcription	Adipose Nuclei	Adipose
42	chr1:155820000-155825200	Strong transcription	Placenta	Placenta
43	chr1:155820000-155825400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:155820000-155825400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:155820000-155825400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:155820200-155824800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:155820200-155824800	Strong transcription	Left Ventricle	heart
48	chr1:155820200-155825000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:155820200-155825400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:155820200-155825400	Strong transcription	Primary hematopoietic stem cells	blood

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