Variant report

Variant	rs9536219
Chromosome Location	chr13:53227301-53227302
allele	C/T
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	chr13:53189348..53193688-chr13:53225267..53228139,8	MCF-7	breast:
2	chr13:53215104..53217509-chr13:53226480..53228845,2	K562	blood:
3	chr13:53191451..53193324-chr13:53224550..53227605,3	MCF-7	breast:
4	chr13:53226555..53228977-chr13:53419370..53422779,3	MCF-7	breast:
5	chr13:53190930..53191973-chr13:53226605..53227465,3	MCF-7	breast:
6	chr13:53225264..53227638-chr2:38976930..38979242,2	MCF-7	breast:
7	chr13:53215104..53218356-chr13:53226198..53228845,3	K562	blood:
8	chr13:53023588..53025754-chr13:53225469..53228375,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000136100	Chromatin interaction
ENSG00000136099	Chromatin interaction
ENSG00000250299	Chromatin interaction
ENSG00000139675	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1057478	0.90[ASW][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap]
rs11616261	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11616459	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11617331	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11618716	0.81[ASW][hapmap];0.89[LWK][hapmap];0.84[MKK][hapmap]
rs1924036	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs2038826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2147676	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2147692	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2575960	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2760815	0.83[CEU][hapmap]
rs342768	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs342770	0.89[ASN][1000 genomes]
rs3742297	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4284531	0.85[CHB][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap]
rs4301905	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4335671	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4884235	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4885325	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs616969	0.87[ASN][1000 genomes]
rs61958118	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6561671	0.87[ASN][1000 genomes]
rs6561675	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7139495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7139630	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs7324427	0.88[ASN][1000 genomes]
rs7328729	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7334137	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7334677	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7336771	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7337021	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7399901	0.90[ASN][1000 genomes]
rs7997186	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7999849	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526951	0.94[ASN][1000 genomes]
rs9526968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526974	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526975	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]
rs9526982	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9536104	0.83[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.87[YRI][hapmap]
rs9536197	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9536200	0.82[ASN][1000 genomes]
rs9536202	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9536211	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9536212	0.92[CHB][hapmap];0.87[JPT][hapmap];0.91[AFR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9536217	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9536220	0.83[CHB][hapmap]
rs9536223	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9536236	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9536247	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9536262	0.90[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap];0.90[ASN][1000 genomes]
rs9563113	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs9563114	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9568750	0.90[ASN][1000 genomes]
rs9568751	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
4	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
5	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
6	nsv819201	chr13:53137490-53240330	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9536219	CKAP2	cis	cerebellum	SCAN
rs9536219	CKAP2	cis	Artery Tibial	GTEx
rs9536219	SUGT1	cis	cerebellum	SCAN
rs9536219	CKAP2	cis	parietal	SCAN
rs9536219	HNRNPA1L2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53224400-53227800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr13:53224400-53228600	Active TSS	H1 Cell Line	embryonic stem cell
3	chr13:53224600-53228600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr13:53224600-53229200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr13:53224800-53228400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr13:53225000-53227800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr13:53225000-53228000	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr13:53225000-53228200	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr13:53225000-53228200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr13:53225000-53228200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr13:53225000-53228200	Active TSS	NHDF-Ad	bronchial
12	chr13:53225000-53228400	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr13:53225000-53228400	Active TSS	Fetal Intestine Small	intestine
14	chr13:53225000-53228600	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr13:53225000-53228600	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr13:53225000-53229000	Active TSS	K562	blood
17	chr13:53225000-53229400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr13:53225200-53228000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr13:53225200-53228000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr13:53225200-53228000	Active TSS	Fetal Kidney	kidney
21	chr13:53225200-53228000	Active TSS	Fetal Stomach	stomach
22	chr13:53225200-53228200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr13:53225200-53228200	Active TSS	Colonic Mucosa	Colon
24	chr13:53225200-53228200	Active TSS	GM12878-XiMat	blood
25	chr13:53225200-53228200	Active TSS	HSMM	muscle
26	chr13:53225200-53228400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr13:53225200-53228400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr13:53225200-53228400	Active TSS	Fetal Intestine Large	intestine
29	chr13:53225200-53228400	Active TSS	Fetal Muscle Trunk	muscle
30	chr13:53225200-53228400	Active TSS	A549	lung
31	chr13:53225200-53228600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr13:53225200-53228600	Active TSS	Hela-S3	cervix
33	chr13:53225400-53227600	Active TSS	Fetal Muscle Leg	muscle
34	chr13:53225400-53227600	Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr13:53225400-53227800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr13:53225400-53227800	Active TSS	Brain Angular Gyrus	brain
37	chr13:53225400-53228000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr13:53225400-53228000	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr13:53225400-53228000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr13:53225400-53228000	Active TSS	Muscle Satellite Cultured Cells	--
41	chr13:53225400-53228000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr13:53225400-53228000	Active TSS	Fetal Brain Male	brain
43	chr13:53225400-53228000	Active TSS	Fetal Heart	heart
44	chr13:53225400-53228000	Active TSS	Fetal Lung	lung
45	chr13:53225400-53228000	Active TSS	Fetal Thymus	thymus
46	chr13:53225400-53228000	Active TSS	Thymus	Thymus
47	chr13:53225400-53228000	Active TSS	NH-A	brain
48	chr13:53225400-53228200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr13:53225400-53228200	Active TSS	Right Ventricle	heart
50	chr13:53225400-53228200	Active TSS	HMEC	breast

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