Variant report

Variant	rs7334677
Chromosome Location	chr13:53231255-53231256
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	chr13:53189836..53192500-chr13:53230172..53233036,2	MCF-7	breast:
2	chr13:53224982..53228384-chr13:53228728..53231432,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139675	Chromatin interaction
ENSG00000250299	Chromatin interaction
ENSG00000165416	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1057478	0.85[CHB][hapmap]
rs11616261	0.87[ASN][1000 genomes]
rs11616459	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11617331	0.80[ASN][1000 genomes]
rs1811894	0.82[ASN][1000 genomes]
rs1811895	0.82[ASN][1000 genomes]
rs1924036	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2038826	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2147676	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2147692	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2575960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs342768	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs342770	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs342778	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3742297	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4284531	0.85[CHB][hapmap]
rs4884235	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4885325	0.80[ASN][1000 genomes]
rs616969	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs61958118	0.80[ASN][1000 genomes]
rs6561671	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6561675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139495	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs7139630	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.88[ASN][1000 genomes]
rs7324427	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7328729	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7334137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7336771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7337021	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7399901	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7997186	0.88[ASN][1000 genomes]
rs7999849	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9526951	0.89[ASN][1000 genomes]
rs9526968	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9526974	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9526975	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs9526982	0.89[ASN][1000 genomes]
rs9536104	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap]
rs9536123	0.88[CEU][hapmap]
rs9536197	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9536200	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9536202	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9536211	0.92[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs9536212	0.92[CHB][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs9536217	0.92[ASN][1000 genomes]
rs9536219	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9536220	0.83[CHB][hapmap]
rs9536223	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9536236	0.89[ASN][1000 genomes]
rs9536247	0.87[ASN][1000 genomes]
rs9536262	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs9563113	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.94[ASN][1000 genomes]
rs9563114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568750	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568751	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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
15	nsv974091	chr13:53230050-53232950	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7334677	CKAP2	cis	cerebellum	SCAN
rs7334677	HNRNPA1L2	cis	cerebellum	SCAN
rs7334677	ALG11	cis	parietal	SCAN
rs7334677	CKAP2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53227600-53235000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:53227800-53238600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:53227800-53238800	Weak transcription	Esophagus	oesophagus
4	chr13:53227800-53260000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr13:53228000-53251000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr13:53228200-53232200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr13:53228200-53256400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr13:53228400-53231800	Weak transcription	Placenta	Placenta
9	chr13:53228400-53232000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr13:53228400-53232000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr13:53228400-53233400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr13:53228400-53233400	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr13:53228400-53234200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr13:53228400-53234200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr13:53228400-53234800	Weak transcription	Aorta	Aorta
16	chr13:53228400-53234800	Weak transcription	Fetal Intestine Small	intestine
17	chr13:53228400-53235400	Weak transcription	Lung	lung
18	chr13:53228400-53236200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr13:53228400-53236200	Weak transcription	HSMMtube	muscle
20	chr13:53228400-53242000	Weak transcription	Thymus	Thymus
21	chr13:53228400-53254600	Weak transcription	Colonic Mucosa	Colon
22	chr13:53228600-53232200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr13:53228600-53232400	Strong transcription	Primary B cells from cord blood	blood
24	chr13:53228600-53254600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr13:53228800-53231800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr13:53228800-53231800	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr13:53228800-53231800	Weak transcription	Fetal Intestine Large	intestine
28	chr13:53228800-53232200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr13:53228800-53232400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr13:53228800-53232400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr13:53228800-53233400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr13:53228800-53234400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr13:53228800-53234400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr13:53228800-53234400	Weak transcription	Psoas Muscle	Psoas
35	chr13:53228800-53234400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr13:53228800-53235000	Weak transcription	Fetal Stomach	stomach
37	chr13:53228800-53237600	Weak transcription	A549	lung
38	chr13:53228800-53240400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr13:53228800-53243400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr13:53228800-53244200	Strong transcription	HSMM	muscle
41	chr13:53229000-53231600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr13:53229000-53231600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr13:53229000-53232400	Weak transcription	K562	blood
44	chr13:53229000-53232600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr13:53229000-53234600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr13:53229000-53236200	Weak transcription	Fetal Kidney	kidney
47	chr13:53229000-53276600	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr13:53229200-53231600	Enhancers	Brain Hippocampus Middle	brain
49	chr13:53229200-53231600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr13:53229200-53231800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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