Variant report

Variant	rs4364717
Chromosome Location	chr9:21801530-21801531
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr9:21801475-21804210	Hela-S3	cervix:	n/a	n/a
2	ZNF263	chr9:21801422-21803458	HEK293-T-REx	kidney:	n/a	chr9:21801626-21801635 chr9:21802599-21802608
3	MXI1	chr9:21801399-21803844	IMR90	lung:	n/a	n/a
4	MAZ	chr9:21801474-21804398	IMR90	lung:	n/a	chr9:21802967-21802977
5	POLR2A	chr9:21801032-21804663	HCT-116	colon:	n/a	n/a
6	KAP1	chr9:21801490-21802011	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:21334810..21337205-chr9:21800546..21802816,2	MCF-7	breast:
2	chr9:21464451..21467378-chr9:21800569..21802345,2	MCF-7	breast:
3	chr9:21796497..21798731-chr9:21800652..21802433,2	MCF-7	breast:
4	chr9:21800247..21802715-chr9:22007122..22010872,3	MCF-7	breast:

Variant related genes	Relation type
MTAP	TF binding region
ENSG00000264545	TF binding region
ENSG00000198642	Chromatin interaction
ENSG00000147883	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10118262	0.80[AMR][1000 genomes]
rs10119568	0.81[EUR][1000 genomes]
rs10119693	0.81[EUR][1000 genomes]
rs10738599	0.82[AMR][1000 genomes]
rs10738601	0.82[EUR][1000 genomes]
rs10757253	0.82[AMR][1000 genomes]
rs10757254	0.82[AMR][1000 genomes]
rs10757255	0.82[AMR][1000 genomes]
rs10757257	0.96[CEU][hapmap];0.82[GIH][hapmap]
rs10811613	0.82[AMR][1000 genomes]
rs10811615	0.90[ASN][1000 genomes]
rs10811617	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10811618	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10811625	0.87[CEU][hapmap]
rs10965122	0.82[AMR][1000 genomes]
rs10965127	0.81[AMR][1000 genomes]
rs10965134	0.86[CEU][hapmap]
rs10965135	0.85[CEU][hapmap]
rs10965143	0.92[CEU][hapmap]
rs10965144	0.92[CEU][hapmap]
rs12344842	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1335505	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs1335512	0.80[AMR][1000 genomes]
rs1345022	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1372057	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs1372058	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs1372059	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs1414228	0.82[AMR][1000 genomes]
rs1414242	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs1414243	0.85[CEU][hapmap]
rs1414244	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs1542074	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1542075	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1542076	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17833407	0.83[CHB][hapmap]
rs1889680	0.81[JPT][hapmap]
rs2123338	0.81[JPT][hapmap]
rs2152272	0.82[AMR][1000 genomes]
rs2152273	0.81[AMR][1000 genomes]
rs2165408	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs2165409	0.85[CEU][hapmap]
rs2184551	0.82[AMR][1000 genomes]
rs2891159	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs3849929	0.82[AMR][1000 genomes]
rs3900787	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs3922992	0.88[CEU][hapmap]
rs3928894	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4352937	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs4548267	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs4636294	0.83[CHB][hapmap]
rs6475576	0.80[AMR][1000 genomes]
rs6475578	0.82[AMR][1000 genomes]
rs6475579	0.82[AMR][1000 genomes]
rs6475585	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7018772	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7021012	0.82[AMR][1000 genomes]
rs7022856	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7023474	1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7023680	0.86[ASN][1000 genomes]
rs7023954	0.88[CEU][hapmap]
rs7024027	0.82[AMR][1000 genomes]
rs7027989	0.85[TSI][hapmap]
rs7033503	0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7037577	0.82[AMR][1000 genomes]
rs7038708	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7045768	0.82[AMR][1000 genomes]
rs72691561	0.85[ASN][1000 genomes]
rs72691562	0.85[ASN][1000 genomes]
rs72691563	0.86[ASN][1000 genomes]
rs72691564	0.86[ASN][1000 genomes]
rs7846749	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7850446	0.80[AMR][1000 genomes]
rs7856941	0.80[AMR][1000 genomes]
rs7866787	0.80[AMR][1000 genomes]
rs7866885	0.80[AMR][1000 genomes]
rs869329	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs869330	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs871024	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9298823	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs935053	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs935055	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9886831	0.81[AMR][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	nsv1026981	chr9:21748202-21811697	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
3	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4364717	IFNA21	cis	parietal	SCAN
rs4364717	MTAP	cis	multi-tissue	Pritchard
rs4364717	MTAP	cis	parietal	SCAN
rs4364717	MLLT3	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21798000-21801600	Weak transcription	Aorta	Aorta
2	chr9:21800000-21801800	Enhancers	Placenta	Placenta
3	chr9:21801000-21801600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:21801000-21801600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:21801000-21801800	Enhancers	Placenta Amnion	Placenta Amnion
6	chr9:21801000-21802000	Enhancers	Spleen	Spleen
7	chr9:21801000-21803400	Active TSS	Stomach Smooth Muscle	stomach
8	chr9:21801200-21801600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:21801200-21801600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:21801200-21801800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:21801200-21801800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr9:21801200-21801800	Enhancers	Primary B cells from peripheral blood	blood
13	chr9:21801200-21801800	Flanking Active TSS	NHDF-Ad	bronchial
14	chr9:21801200-21802000	Flanking Active TSS	Colon Smooth Muscle	Colon
15	chr9:21801200-21802000	Flanking Active TSS	HMEC	breast
16	chr9:21801200-21802000	Flanking Active TSS	NHEK	skin
17	chr9:21801400-21801600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr9:21801400-21801600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
19	chr9:21801400-21801600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:21801400-21801600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
21	chr9:21801400-21801600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
22	chr9:21801400-21801600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:21801400-21801600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:21801400-21801600	Active TSS	Primary B cells from cord blood	blood
25	chr9:21801400-21801600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr9:21801400-21801600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr9:21801400-21801600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:21801400-21801600	Active TSS	Adipose Nuclei	Adipose
29	chr9:21801400-21801600	Enhancers	Brain Cingulate Gyrus	brain
30	chr9:21801400-21801600	Flanking Active TSS	Brain Germinal Matrix	brain
31	chr9:21801400-21801600	Enhancers	Brain Hippocampus Middle	brain
32	chr9:21801400-21801600	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr9:21801400-21801600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr9:21801400-21801600	Enhancers	Fetal Intestine Large	intestine
35	chr9:21801400-21801600	Enhancers	Hela-S3	cervix
36	chr9:21801400-21801600	Active TSS	HSMM	muscle
37	chr9:21801400-21801600	Enhancers	HUVEC	blood vessel
38	chr9:21801400-21801800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
39	chr9:21801400-21801800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr9:21801400-21801800	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr9:21801400-21801800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr9:21801400-21801800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr9:21801400-21801800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr9:21801400-21801800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:21801400-21801800	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr9:21801400-21801800	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
47	chr9:21801400-21802000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr9:21801400-21802000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr9:21801400-21802000	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr9:21801400-21802000	Flanking Active TSS	Duodenum Mucosa	Duodenum

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