Variant report

Variant	rs7023954
Chromosome Location	chr9:21816758-21816759
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:21815923..21817929-chr9:22242697..22244990,2	MCF-7	breast:
2	chr9:21800813..21805862-chr9:21815237..21818014,5	MCF-7	breast:
3	chr9:21815119..21818552-chr9:22084345..22087438,5	MCF-7	breast:
4	chr9:21814236..21815756-chr9:21816687..21818774,2	MCF-7	breast:
5	chr9:21811237..21820561-chr9:21988636..21997115,18	MCF-7	breast:
6	chr9:21811532..21820564-chr9:21988281..21997291,17	MCF-7	breast:
7	chr9:21815068..21816842-chr9:22213097..22214603,2	MCF-7	breast:
8	chr9:21814593..21817244-chr9:22101346..22103643,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000266446	Chromatin interaction
ENSG00000264545	Chromatin interaction
ENSG00000147889	Chromatin interaction
ENSG00000099810	Chromatin interaction
ENSG00000240498	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10114559	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119568	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10119693	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10121449	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10121899	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10738598	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10738601	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10757257	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10811623	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10811625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10811626	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10811629	1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs10965128	0.89[ASN][1000 genomes]
rs10965133	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10965134	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10965135	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10965141	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10965143	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10965144	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10965145	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10965153	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs11523031	0.93[ASN][1000 genomes]
rs11532907	0.85[ASN][1000 genomes]
rs1335511	0.81[AMR][1000 genomes]
rs1341866	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1345020	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1345023	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1345024	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1414243	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs1414253	0.80[EUR][1000 genomes]
rs2165409	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs3900787	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]
rs3922992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4265275	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4364717	0.88[CEU][hapmap]
rs4615669	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4977567	0.91[ASN][1000 genomes]
rs4977733	0.93[ASN][1000 genomes]
rs58377678	0.91[ASN][1000 genomes]
rs7022754	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7023329	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.92[ASN][1000 genomes]
rs7029036	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7033879	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7038523	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7049092	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7863090	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7863942	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7868783	0.93[ASN][1000 genomes]
rs958219	0.80[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7023954	IFNA21	cis	parietal	SCAN
rs7023954	MTAP	cis	parietal	SCAN
rs7023954	MTAP	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21804000-21817600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:21804000-21838200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:21806000-21817600	Genic enhancers	HMEC	breast
4	chr9:21806400-21819800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:21806600-21841200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:21809200-21836800	Weak transcription	Small Intestine	intestine
7	chr9:21812200-21817000	Weak transcription	Fetal Intestine Small	intestine
8	chr9:21812200-21817200	Weak transcription	Esophagus	oesophagus
9	chr9:21812200-21817400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:21812800-21817400	Weak transcription	Right Ventricle	heart
11	chr9:21813600-21817000	Weak transcription	Colonic Mucosa	Colon
12	chr9:21813800-21817400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr9:21814000-21817200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:21814000-21817400	Weak transcription	Right Atrium	heart
15	chr9:21814000-21831800	Weak transcription	Fetal Heart	heart
16	chr9:21814400-21817600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr9:21814400-21831800	Weak transcription	Stomach Mucosa	stomach
18	chr9:21814400-21837400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr9:21814400-21845200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr9:21814600-21817400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr9:21814600-21817800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr9:21814600-21818600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr9:21814600-21819200	Strong transcription	Dnd41	blood
24	chr9:21814800-21817000	Strong transcription	HSMM	muscle
25	chr9:21814800-21819600	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:21814800-21819800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:21814800-21820000	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr9:21814800-21820000	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr9:21814800-21820400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr9:21815000-21817000	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr9:21815000-21818600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:21815000-21819200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr9:21815000-21819200	Strong transcription	NHEK	skin
34	chr9:21815000-21819400	ZNF genes & repeats	A549	lung
35	chr9:21815000-21819400	Strong transcription	NH-A	brain
36	chr9:21815000-21819600	Strong transcription	Primary B cells from peripheral blood	blood
37	chr9:21815000-21819800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr9:21815200-21819600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr9:21815400-21818400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr9:21815400-21819200	Strong transcription	Hela-S3	cervix
41	chr9:21815400-21819400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr9:21815400-21819400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr9:21815600-21816800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:21815600-21816800	Strong transcription	Brain Angular Gyrus	brain
45	chr9:21815600-21816800	Strong transcription	Osteobl	bone
46	chr9:21815600-21817200	Strong transcription	Left Ventricle	heart
47	chr9:21815600-21817400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr9:21815600-21817400	Genic enhancers	Liver	Liver
49	chr9:21815600-21817400	Strong transcription	Colon Smooth Muscle	Colon
50	chr9:21815600-21817600	Strong transcription	GM12878-XiMat	blood

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