Variant report

Variant	rs3928894
Chromosome Location	chr9:21818310-21818311
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:21815119..21818552-chr9:22084345..22087438,5	MCF-7	breast:
2	chr9:21814236..21815756-chr9:21816687..21818774,2	MCF-7	breast:
3	chr9:21811237..21820561-chr9:21988636..21997115,18	MCF-7	breast:
4	chr9:21811828..21813353-chr9:21817709..21820249,2	MCF-7	breast:
5	chr9:21811532..21820564-chr9:21988281..21997291,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229298	Chromatin interaction
ENSG00000266446	Chromatin interaction
ENSG00000240498	Chromatin interaction
ENSG00000147889	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10118262	0.81[ASN][1000 genomes]
rs10119658	0.81[ASN][1000 genomes]
rs10738599	0.86[ASN][1000 genomes]
rs10757250	0.81[ASN][1000 genomes]
rs10757251	0.80[ASN][1000 genomes]
rs10757252	0.81[ASN][1000 genomes]
rs10757253	0.86[ASN][1000 genomes]
rs10757254	0.86[ASN][1000 genomes]
rs10757255	0.86[ASN][1000 genomes]
rs10811613	0.86[ASN][1000 genomes]
rs10811615	0.94[ASN][1000 genomes]
rs10811617	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10811618	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10965122	0.86[ASN][1000 genomes]
rs10965127	0.86[ASN][1000 genomes]
rs12344842	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1335505	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs1335512	0.82[ASN][1000 genomes]
rs1345022	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1372057	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs1372058	0.89[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs1372059	0.89[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs1414228	0.86[ASN][1000 genomes]
rs1414229	0.86[ASN][1000 genomes]
rs1414242	0.82[ASW][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap]
rs1414244	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs1414250	0.81[ASN][1000 genomes]
rs1414251	0.81[ASN][1000 genomes]
rs1414252	0.81[ASN][1000 genomes]
rs1414256	0.81[ASN][1000 genomes]
rs1414257	0.81[ASN][1000 genomes]
rs1440993	0.86[ASN][1000 genomes]
rs1542074	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1542075	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1542076	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17833407	0.83[CHB][hapmap]
rs1889680	0.85[JPT][hapmap]
rs1932237	0.80[ASN][1000 genomes]
rs2123338	0.85[JPT][hapmap]
rs2152272	0.85[ASN][1000 genomes]
rs2152273	0.86[ASN][1000 genomes]
rs2165408	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs2184551	0.86[ASN][1000 genomes]
rs2218220	0.81[ASN][1000 genomes]
rs2891159	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs3849929	0.86[ASN][1000 genomes]
rs3927737	0.89[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3927738	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4300088	0.81[ASN][1000 genomes]
rs4352937	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs4364717	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4431674	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4548267	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs4636294	0.82[ASW][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap]
rs6475576	0.85[ASN][1000 genomes]
rs6475578	0.86[ASN][1000 genomes]
rs6475579	0.86[ASN][1000 genomes]
rs6475585	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7018772	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7021012	0.84[ASN][1000 genomes]
rs7022856	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7023329	0.84[CEU][hapmap]
rs7023474	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7023680	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024027	0.86[ASN][1000 genomes]
rs7027989	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7033503	0.82[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.91[ASN][1000 genomes]
rs7037577	0.85[ASN][1000 genomes]
rs7038708	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7045768	0.86[ASN][1000 genomes]
rs72691561	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72691562	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72691563	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72691564	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7846749	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7850446	0.85[ASN][1000 genomes]
rs7852450	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7852710	0.81[ASN][1000 genomes]
rs7856941	0.80[ASN][1000 genomes]
rs7866540	0.83[ASN][1000 genomes]
rs7866787	0.81[ASN][1000 genomes]
rs7866885	0.80[ASN][1000 genomes]
rs869329	0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs869330	1.00[ASW][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs871024	1.00[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9298823	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs935053	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs935055	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9886831	0.86[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	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3928894	MTAP	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21804000-21838200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:21806400-21819800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr9:21806600-21841200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:21809200-21836800	Weak transcription	Small Intestine	intestine
5	chr9:21814000-21831800	Weak transcription	Fetal Heart	heart
6	chr9:21814400-21831800	Weak transcription	Stomach Mucosa	stomach
7	chr9:21814400-21837400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr9:21814400-21845200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr9:21814600-21818600	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:21814600-21819200	Strong transcription	Dnd41	blood
11	chr9:21814800-21819600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr9:21814800-21819800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:21814800-21820000	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr9:21814800-21820000	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr9:21814800-21820400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:21815000-21818600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:21815000-21819200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr9:21815000-21819200	Strong transcription	NHEK	skin
19	chr9:21815000-21819400	ZNF genes & repeats	A549	lung
20	chr9:21815000-21819400	Strong transcription	NH-A	brain
21	chr9:21815000-21819600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr9:21815000-21819800	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr9:21815200-21819600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:21815400-21818400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr9:21815400-21819200	Strong transcription	Hela-S3	cervix
26	chr9:21815400-21819400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr9:21815400-21819400	Strong transcription	Duodenum Mucosa	Duodenum
28	chr9:21815600-21818400	Strong transcription	Aorta	Aorta
29	chr9:21815600-21818800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr9:21815600-21819000	Strong transcription	Fetal Lung	lung
31	chr9:21815600-21819000	Strong transcription	HSMMtube	muscle
32	chr9:21815600-21819200	Strong transcription	Primary T cells from cord blood	blood
33	chr9:21815600-21819200	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr9:21815600-21819200	Strong transcription	HepG2	liver
35	chr9:21815600-21819400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr9:21815600-21819400	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr9:21815600-21819400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr9:21815600-21819400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr9:21815600-21819400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr9:21815600-21819400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr9:21815600-21819400	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr9:21815600-21819400	Strong transcription	Placenta	Placenta
43	chr9:21815600-21819400	Strong transcription	Fetal Stomach	stomach
44	chr9:21815600-21819600	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr9:21815600-21819600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr9:21815600-21819600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr9:21815600-21819600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr9:21815600-21819600	Strong transcription	Adipose Nuclei	Adipose
49	chr9:21815600-21819600	Strong transcription	Brain Substantia Nigra	brain
50	chr9:21815600-21819600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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