Variant report

Variant	rs7990581
Chromosome Location	chr13:53019433-53019434
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:53017677..53022269-chr13:53022442..53026165,6	MCF-7	breast:
2	chr13:53015538..53018877-chr13:53019093..53022544,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136100	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1056335	0.86[CHB][hapmap]
rs11148252	0.91[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11618716	1.00[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.84[LWK][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.94[YRI][hapmap];0.83[EUR][1000 genomes]
rs11620062	0.89[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1327323	0.81[CHB][hapmap]
rs3803264	0.85[CHB][hapmap]
rs3886077	1.00[ASW][hapmap];0.82[CEU][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs3892337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4286007	1.00[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4884320	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs4884354	0.90[CHB][hapmap]
rs4884452	0.91[ASW][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];0.94[YRI][hapmap]
rs4885953	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs4886018	0.91[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4886077	0.90[CHB][hapmap]
rs6561664	0.80[ASN][1000 genomes]
rs6561665	0.86[CHB][hapmap]
rs6561666	0.88[ASN][1000 genomes]
rs7321964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7323666	0.90[CHB][hapmap]
rs7328653	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7333451	0.90[CHB][hapmap]
rs7334583	0.88[ASN][1000 genomes]
rs7336679	0.90[CHB][hapmap]
rs7987115	0.91[ASW][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap];0.88[YRI][hapmap]
rs7993748	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs8001624	0.90[CHB][hapmap]
rs9379	0.86[CHB][hapmap]
rs9526913	1.00[ASW][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];0.87[MKK][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs9526927	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9536046	0.86[CHB][hapmap]
rs9536048	0.86[CHB][hapmap]
rs9536052	0.86[CHB][hapmap]
rs9536066	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9536079	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9536104	0.82[MKK][hapmap]
rs9568732	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568734	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9596643	0.84[CHB][hapmap]
rs9596648	0.86[CHB][hapmap]
rs9596649	0.88[ASN][1000 genomes]
rs9596651	0.86[CHB][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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 target site	54 gene(s)	inside rSNPs	diseases
4	nsv428288	chr13:52728370-53068132	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv900084	chr13:52835231-53119704	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv1838257	chr13:52971893-53231454	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	esv3434605	chr13:52999509-53034851	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	n/a

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7990581	CKAP2	cis	Artery Tibial	GTEx
rs7990581	CKAP2	cis	Adipose Subcutaneous	GTEx
rs7990581	HNRNPA1L2	cis	parietal	SCAN
rs7990581	HNRNPA1L2	cis	cerebellum	SCAN
rs7990581	CKAP2	cis	Heart Left Ventricle	GTEx
rs7990581	CKAP2	cis	parietal	SCAN
rs7990581	CKAP2	cis	Nerve Tibial	GTEx
rs7990581	CKAP2	cis	cerebellum	SCAN
rs7990581	LECT1	cis	parietal	SCAN
rs7990581	CKAP2	cis	Skin Sun Exposed Lower leg	GTEx
rs7990581	CKAP2	cis	Thyroid	GTEx
rs7990581	CKAP2	cis	Muscle Skeletal	GTEx
rs7990581	CKAP2	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52980200-53021600	Weak transcription	Small Intestine	intestine
2	chr13:52981000-53022800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr13:52984400-53023400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr13:52987200-53023600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr13:52989000-53021600	Weak transcription	Fetal Heart	heart
6	chr13:52989000-53022800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:52995200-53023800	Weak transcription	Aorta	Aorta
8	chr13:52995800-53019800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr13:52995800-53023800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr13:52999000-53022400	Weak transcription	Right Ventricle	heart
11	chr13:53000600-53022200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr13:53001800-53022200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr13:53003800-53021600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr13:53003800-53021600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr13:53003800-53021600	Weak transcription	Right Atrium	heart
16	chr13:53003800-53022000	Weak transcription	Brain Substantia Nigra	brain
17	chr13:53003800-53022400	Weak transcription	Psoas Muscle	Psoas
18	chr13:53008600-53019600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr13:53008600-53023600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr13:53008800-53021800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr13:53008800-53022200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr13:53009200-53022400	Weak transcription	Brain Germinal Matrix	brain
23	chr13:53010200-53022800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr13:53010600-53021600	Weak transcription	Esophagus	oesophagus
25	chr13:53010600-53021800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr13:53010600-53022200	Weak transcription	Stomach Mucosa	stomach
27	chr13:53011400-53021600	Weak transcription	A549	lung
28	chr13:53013000-53021600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr13:53013000-53021600	Weak transcription	Hela-S3	cervix
30	chr13:53013200-53022200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr13:53013200-53022400	Weak transcription	Fetal Brain Male	brain
32	chr13:53013400-53020400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr13:53013400-53021600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr13:53013400-53021600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr13:53013400-53021600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr13:53013400-53021600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr13:53013400-53022200	Weak transcription	Brain Angular Gyrus	brain
38	chr13:53013400-53022800	Weak transcription	NHLF	lung
39	chr13:53013400-53023400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr13:53013600-53020400	Weak transcription	K562	blood
41	chr13:53013800-53021600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr13:53014800-53022600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr13:53015400-53021600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr13:53015400-53021600	Weak transcription	Fetal Lung	lung
45	chr13:53015400-53021600	Weak transcription	Spleen	Spleen
46	chr13:53015400-53022200	Weak transcription	Fetal Brain Female	brain
47	chr13:53015400-53022200	Weak transcription	Gastric	stomach
48	chr13:53015400-53022200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr13:53015400-53023200	Weak transcription	Colonic Mucosa	Colon
50	chr13:53015400-53023400	Weak transcription	Fetal Kidney	kidney

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