Variant report

Variant	rs9625575
Chromosome Location	chr22:29204886-29204887
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29168673..29170416-chr22:29204780..29206818,2	MCF-7	breast:
2	chr22:28994581..28996472-chr22:29204269..29206724,2	MCF-7	breast:
3	chr22:29203783..29206690-chr22:29212432..29214598,2	K562	blood:
4	chr22:29133437..29141650-chr22:29203240..29216422,34	MCF-7	breast:
5	chr22:29126583..29142031-chr22:29203252..29220632,67	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226471	Chromatin interaction
ENSG00000100209	Chromatin interaction
ENSG00000183765	Chromatin interaction
ENSG00000159873	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10427858	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12330071	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17880929	1.00[AFR][1000 genomes]
rs2206061	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2228260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2235432	0.91[JPT][hapmap]
rs41281603	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56119508	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5752839	1.00[MEX][hapmap]
rs5762893	1.00[MEX][hapmap]
rs5762900	1.00[MEX][hapmap]
rs5762906	1.00[MEX][hapmap]
rs5997401	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6005861	1.00[CEU][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6005868	0.91[JPT][hapmap]
rs6005870	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6005874	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005898	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005899	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005923	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6005924	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6005926	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7288513	1.00[MEX][hapmap]
rs7290364	1.00[MEX][hapmap]
rs9306460	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9625551	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9625565	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9625580	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9625645	1.00[MEX][hapmap]
rs9625657	1.00[MEX][hapmap]

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	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9625575	LOC388890	cis	multi-tissue	Pritchard

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29197000-29205400	Weak transcription	Spleen	Spleen
2	chr22:29197200-29208200	Weak transcription	Esophagus	oesophagus
3	chr22:29197200-29209800	Weak transcription	Left Ventricle	heart
4	chr22:29197200-29214200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr22:29197200-29231600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr22:29197400-29214400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr22:29197400-29220400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr22:29197600-29209800	Weak transcription	Ovary	ovary
9	chr22:29197800-29214200	Weak transcription	Right Ventricle	heart
10	chr22:29198000-29225200	Weak transcription	HSMM	muscle
11	chr22:29198200-29218600	Weak transcription	Brain Angular Gyrus	brain
12	chr22:29198400-29206200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr22:29198400-29208200	Weak transcription	Fetal Lung	lung
14	chr22:29198400-29208400	Weak transcription	Lung	lung
15	chr22:29198400-29209800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr22:29198400-29214000	Weak transcription	Colonic Mucosa	Colon
17	chr22:29198400-29214400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr22:29198400-29215600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr22:29198400-29225200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr22:29198600-29206800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr22:29198600-29207200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr22:29198600-29207200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr22:29198600-29210600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr22:29198600-29211200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr22:29198600-29212600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr22:29198600-29214200	Weak transcription	Colon Smooth Muscle	Colon
27	chr22:29198600-29214400	Weak transcription	Aorta	Aorta
28	chr22:29198600-29214600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr22:29198600-29219400	Weak transcription	NHLF	lung
30	chr22:29198600-29225200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr22:29198600-29225200	Weak transcription	Osteobl	bone
32	chr22:29198600-29231400	Weak transcription	HSMMtube	muscle
33	chr22:29198800-29205600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr22:29198800-29205800	Weak transcription	Primary B cells from cord blood	blood
35	chr22:29198800-29206800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr22:29198800-29207200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr22:29198800-29207800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr22:29198800-29214200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr22:29198800-29214400	Weak transcription	Fetal Heart	heart
40	chr22:29198800-29230800	Weak transcription	NHEK	skin
41	chr22:29199000-29206200	Weak transcription	GM12878-XiMat	blood
42	chr22:29199000-29208400	Weak transcription	NHDF-Ad	bronchial
43	chr22:29199400-29207400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr22:29200600-29206000	Enhancers	Placenta	Placenta
45	chr22:29200600-29231400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr22:29200800-29205200	Weak transcription	Thymus	Thymus
47	chr22:29200800-29208200	Weak transcription	Fetal Stomach	stomach
48	chr22:29201000-29206600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr22:29202400-29206600	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr22:29203200-29206600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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