Variant report

Variant	rs3900787
Chromosome Location	chr9:21828110-21828111
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:21827202..21829745-chr9:22105278..22107397,2	MCF-7	breast:
2	chr9:21827752..21829357-chr9:22103639..22105234,2	MCF-7	breast:
3	chr9:21827757..21830493-chr9:21833555..21836512,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10114559	0.91[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10119568	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10119693	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10121449	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121899	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10738598	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10738601	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10757257	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10811623	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10811625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10811626	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10811629	0.81[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.86[LWK][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap];0.94[ASN][1000 genomes]
rs10965128	0.88[ASN][1000 genomes]
rs10965133	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10965134	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10965135	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10965141	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10965143	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10965144	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10965145	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10965153	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs11523031	0.92[ASN][1000 genomes]
rs11532907	0.85[ASN][1000 genomes]
rs1341866	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1345020	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1345023	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1345024	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1414243	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap]
rs2165409	0.88[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap]
rs3922992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4265275	0.85[EUR][1000 genomes]
rs4364717	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs4615669	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4636295	0.82[YRI][hapmap]
rs4977567	0.91[ASN][1000 genomes]
rs4977733	0.94[ASN][1000 genomes]
rs58377678	0.90[ASN][1000 genomes]
rs7022754	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7023329	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[ASN][1000 genomes]
rs7023954	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7029036	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7033879	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7038523	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7049092	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7850937	0.83[GIH][hapmap]
rs7851133	0.83[GIH][hapmap];0.82[YRI][hapmap]
rs7863090	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7863942	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7868783	0.94[ASN][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	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
3	esv33626	chr9:21827421-21828357	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3900787	IFNA21	cis	parietal	SCAN
rs3900787	MTAP	cis	multi-tissue	Pritchard
rs3900787	MTAP	cis	parietal	SCAN

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	chr9:21806600-21841200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:21809200-21836800	Weak transcription	Small Intestine	intestine
4	chr9:21814000-21831800	Weak transcription	Fetal Heart	heart
5	chr9:21814400-21831800	Weak transcription	Stomach Mucosa	stomach
6	chr9:21814400-21837400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr9:21814400-21845200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr9:21816400-21836600	Weak transcription	Psoas Muscle	Psoas
9	chr9:21816600-21833800	Weak transcription	Fetal Brain Male	brain
10	chr9:21816800-21833200	Weak transcription	Brain Angular Gyrus	brain
11	chr9:21817400-21829000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr9:21817400-21830200	Weak transcription	Colon Smooth Muscle	Colon
13	chr9:21817400-21837800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr9:21817800-21840600	Weak transcription	Colonic Mucosa	Colon
15	chr9:21818600-21840800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr9:21818800-21840400	Weak transcription	Right Ventricle	heart
17	chr9:21819000-21828800	Weak transcription	HSMMtube	muscle
18	chr9:21819000-21831400	Weak transcription	NHLF	lung
19	chr9:21819200-21828800	Weak transcription	Osteobl	bone
20	chr9:21819400-21829000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr9:21819400-21829200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr9:21819400-21830800	Weak transcription	HUVEC	blood vessel
23	chr9:21819400-21831400	Weak transcription	Placenta	Placenta
24	chr9:21819400-21831800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr9:21819400-21833800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr9:21819400-21840400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr9:21819400-21841600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr9:21819600-21830600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr9:21819800-21832400	Weak transcription	Brain Anterior Caudate	brain
30	chr9:21823000-21830600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr9:21823800-21840400	Strong transcription	Fetal Muscle Leg	muscle
32	chr9:21824000-21830000	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr9:21824000-21830800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr9:21824000-21831200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr9:21824200-21840400	Strong transcription	Fetal Lung	lung
36	chr9:21824400-21828400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr9:21824400-21828800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:21824400-21830200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr9:21824400-21831000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr9:21824400-21831000	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr9:21824400-21831200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr9:21824400-21831400	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr9:21824600-21829200	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr9:21824600-21829600	Strong transcription	Liver	Liver
45	chr9:21824600-21831200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:21824600-21831200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr9:21824800-21828400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr9:21824800-21829400	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr9:21824800-21830200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr9:21824800-21831200	Strong transcription	Primary T helper cells PMA-I stimulated	--

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