Variant report

Variant	rs9526975
Chromosome Location	chr13:53255804-53255805
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:53253633..53256352-chr13:53264459..53267100,2	K562	blood:
2	chr13:53225756..53229849-chr13:53255678..53259863,4	K562	blood:

Variant related genes	Relation type
ENSG00000165416	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1057478	1.00[ASW][hapmap];0.87[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11616261	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11616459	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11617331	0.84[ASN][1000 genomes]
rs1924036	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs2038826	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2147676	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2147692	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2575960	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2760815	0.96[CEU][hapmap]
rs342768	0.87[ASN][1000 genomes]
rs342770	0.87[ASN][1000 genomes]
rs3742297	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4284531	0.87[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs4301905	0.80[ASN][1000 genomes]
rs4335671	0.80[ASN][1000 genomes]
rs4884235	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs4885325	0.84[ASN][1000 genomes]
rs616969	0.85[ASN][1000 genomes]
rs61958118	0.84[ASN][1000 genomes]
rs6561671	0.85[ASN][1000 genomes]
rs6561675	0.89[ASN][1000 genomes]
rs7139495	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7139630	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7324427	0.90[ASN][1000 genomes]
rs7328729	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7334137	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs7334677	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs7336771	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs7337021	0.93[ASN][1000 genomes]
rs7399901	0.88[ASN][1000 genomes]
rs7997186	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7999849	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526951	0.92[ASN][1000 genomes]
rs9526968	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526974	0.90[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526979	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9526982	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9536104	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];0.86[YRI][hapmap]
rs9536197	0.85[ASN][1000 genomes]
rs9536202	0.90[ASN][1000 genomes]
rs9536211	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9536212	0.92[CHB][hapmap];0.87[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9536217	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9536219	0.90[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9536220	0.85[CEU][hapmap];0.83[CHB][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9536223	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9536236	0.88[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9536242	0.84[EUR][1000 genomes]
rs9536247	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9536262	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9563113	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs9563114	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs9568750	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568751	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv820041	chr13:53061338-53280588	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv1044949	chr13:53071140-53289426	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1044051	chr13:53139132-53287023	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1038942	chr13:53139132-53289426	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1039911	chr13:53139132-53303074	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv1037189	chr13:53173013-53287060	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv541775	chr13:53173013-53287060	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv1047265	chr13:53173013-53311419	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv541776	chr13:53173013-53311419	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
13	nsv900088	chr13:53250839-53274936	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9526975	CKAP2	cis	Nerve Tibial	GTEx
rs9526975	HNRNPA1L2	cis	parietal	SCAN
rs9526975	CKAP2	cis	parietal	SCAN
rs9526975	CKAP2	cis	Artery Tibial	GTEx
rs9526975	HNRNPA1L2	cis	cerebellum	SCAN
rs9526975	CKAP2	cis	cerebellum	SCAN
rs9526975	SUGT1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53227800-53260000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:53228200-53256400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr13:53229000-53276600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr13:53229200-53268000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr13:53230200-53263600	Weak transcription	Stomach Mucosa	stomach
6	chr13:53230400-53266400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr13:53230600-53266400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr13:53230800-53277400	Weak transcription	Gastric	stomach
9	chr13:53231200-53262400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr13:53231800-53266400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr13:53235200-53276000	Weak transcription	Right Ventricle	heart
12	chr13:53237200-53261800	Weak transcription	Fetal Brain Male	brain
13	chr13:53239200-53265600	Weak transcription	Brain Angular Gyrus	brain
14	chr13:53240600-53264200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr13:53240600-53275800	Weak transcription	K562	blood
16	chr13:53242600-53258000	Weak transcription	Small Intestine	intestine
17	chr13:53242800-53278600	Weak transcription	Psoas Muscle	Psoas
18	chr13:53243200-53259000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr13:53243800-53258200	Weak transcription	NHEK	skin
20	chr13:53245400-53257200	Strong transcription	Primary B cells from cord blood	blood
21	chr13:53245400-53263800	Strong transcription	Dnd41	blood
22	chr13:53245600-53263600	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr13:53248400-53265200	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr13:53248600-53263400	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr13:53248600-53265200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr13:53249000-53256200	Strong transcription	Primary T cells from cord blood	blood
27	chr13:53249000-53257400	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr13:53249000-53263400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr13:53249000-53263400	Strong transcription	Duodenum Mucosa	Duodenum
30	chr13:53249000-53263600	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr13:53249000-53266400	Strong transcription	Liver	Liver
32	chr13:53249000-53266400	Strong transcription	Fetal Intestine Large	intestine
33	chr13:53249000-53266600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr13:53249000-53267400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr13:53249200-53257400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr13:53249200-53257800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr13:53249200-53259400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr13:53249200-53261000	Strong transcription	Adipose Nuclei	Adipose
39	chr13:53249200-53263400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr13:53249200-53265200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr13:53249600-53257000	Strong transcription	HepG2	liver
42	chr13:53249600-53257400	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr13:53249600-53262800	Strong transcription	Fetal Thymus	thymus
44	chr13:53249800-53256800	Strong transcription	HUVEC	blood vessel
45	chr13:53249800-53266000	Strong transcription	Primary B cells from peripheral blood	blood
46	chr13:53250000-53263800	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr13:53250000-53265000	Weak transcription	Hela-S3	cervix
48	chr13:53250400-53256200	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr13:53250400-53257200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr13:53250400-53262400	Strong transcription	Placenta	Placenta

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