Variant report

Variant	rs2296347
Chromosome Location	chr13:52728423-52728424
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52725842..52728742-chr13:52731896..52733455,2	MCF-7	breast:
2	chr13:52726747..52729442-chr13:52731857..52734601,2	K562	blood:

Variant related genes	Relation type
ENSG00000136098	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1004576	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.95[YRI][hapmap];0.98[ASN][1000 genomes]
rs1055062	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1060631	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1134727	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11620583	0.87[CHB][hapmap]
rs12146904	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.98[ASN][1000 genomes]
rs12431310	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs12560598	0.88[ASN][1000 genomes]
rs1327323	0.87[MEX][hapmap]
rs1571189	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1801243	0.91[CHB][hapmap]
rs1886538	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs1886539	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886542	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1886543	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1886544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1886545	0.89[ASN][1000 genomes]
rs1886546	0.88[ASN][1000 genomes]
rs1886547	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1924611	0.86[CHB][hapmap]
rs2004866	0.91[CHB][hapmap]
rs2005182	0.95[ASN][1000 genomes]
rs2181891	0.91[CHB][hapmap]
rs2274202	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2277448	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2296348	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2296349	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2408544	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2408546	0.92[ASN][1000 genomes]
rs2408547	0.93[ASN][1000 genomes]
rs2408548	0.93[ASN][1000 genomes]
rs2408550	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2408551	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2408552	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.90[ASN][1000 genomes]
rs2408554	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2408609	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2408611	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2897964	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2897965	0.92[ASN][1000 genomes]
rs2897977	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3368	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3742289	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3742291	0.88[ASN][1000 genomes]
rs3783242	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3818422	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3825528	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs4261421	0.92[ASN][1000 genomes]
rs4264295	0.92[ASN][1000 genomes]
rs4297592	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs4497567	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4941727	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4943060	0.87[ASN][1000 genomes]
rs61958804	0.89[ASN][1000 genomes]
rs61958805	0.86[ASN][1000 genomes]
rs6561656	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6561658	0.81[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6561665	0.87[MEX][hapmap]
rs6650384	0.93[ASN][1000 genomes]
rs6650385	0.93[ASN][1000 genomes]
rs66849828	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7318287	0.92[ASN][1000 genomes]
rs7319784	0.85[ASN][1000 genomes]
rs7320252	0.93[ASN][1000 genomes]
rs7320429	0.93[ASN][1000 genomes]
rs732071	0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs7320831	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7321120	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7321310	0.85[ASN][1000 genomes]
rs7321435	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs7324458	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7327634	0.91[CHB][hapmap]
rs7332356	0.88[ASN][1000 genomes]
rs7338131	0.93[ASN][1000 genomes]
rs747781	0.91[CHB][hapmap]
rs755363	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7981050	0.87[MEX][hapmap]
rs7981904	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7991237	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7995946	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7998770	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9316563	0.87[CHB][hapmap]
rs9526819	0.87[CHB][hapmap]
rs9526823	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9526825	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9526826	0.93[ASN][1000 genomes]
rs9526834	0.94[ASN][1000 genomes]
rs9526835	0.92[ASN][1000 genomes]
rs9526836	0.98[ASN][1000 genomes]
rs9526837	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9526841	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526842	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs9526843	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535812	0.91[CHB][hapmap]
rs9535822	0.86[CHB][hapmap]
rs9535825	0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap]
rs9535826	0.87[CHB][hapmap]
rs9535832	0.91[CHB][hapmap]
rs9535836	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535845	0.93[ASN][1000 genomes]
rs9535851	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535853	0.88[ASN][1000 genomes]
rs9535856	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535858	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535861	0.91[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.82[ASN][1000 genomes]
rs9535862	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535866	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535867	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9535871	0.93[ASN][1000 genomes]
rs9535873	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.95[YRI][hapmap];0.98[ASN][1000 genomes]
rs9535878	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535879	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs9535880	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535882	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535883	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535885	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs9535887	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535888	0.87[ASN][1000 genomes]
rs9535889	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9563089	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9568682	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs9568684	0.89[JPT][hapmap]
rs9568692	0.93[ASN][1000 genomes]
rs9568713	0.91[CHB][hapmap];0.82[JPT][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	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv1037567	chr13:52643647-52802799	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	esv3429935	chr13:52694751-52735744	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2296347	VPS36	cis	cerebellum	SCAN
rs2296347	CKAP2	cis	multi-tissue	Pritchard
rs2296347	NEK3	cis	Muscle Skeletal	GTEx
rs2296347	NEK3	cis	multi-tissue	Pritchard
rs2296347	NEK3	cis	normal skin	skin_eQTL
rs2296347	LOC440138	cis	multi-tissue	Pritchard
rs2296347	CKAP2	cis	cerebellum	SCAN
rs2296347	CKAP2	cis	parietal	SCAN
rs2296347	NEK3	cis	Adipose Subcutaneous	GTEx
rs2296347	LECT1	cis	parietal	SCAN
rs2296347	NEK3	Cis_1M	lymphoblastoid	RTeQTL
rs2296347	ATP7B	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52703600-52730800	Weak transcription	Stomach Mucosa	stomach
2	chr13:52703600-52731000	Weak transcription	Brain Angular Gyrus	brain
3	chr13:52703600-52732600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr13:52703600-52732800	Weak transcription	Psoas Muscle	Psoas
5	chr13:52703600-52733000	Weak transcription	Esophagus	oesophagus
6	chr13:52703800-52731200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr13:52703800-52731400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr13:52703800-52731400	Weak transcription	Spleen	Spleen
9	chr13:52703800-52732600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr13:52703800-52732600	Weak transcription	HMEC	breast
11	chr13:52703800-52733200	Weak transcription	Gastric	stomach
12	chr13:52704000-52733000	Weak transcription	Fetal Thymus	thymus
13	chr13:52704800-52730000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr13:52706200-52731000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr13:52706600-52730800	Weak transcription	HUVEC	blood vessel
16	chr13:52706600-52731000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr13:52706600-52732600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr13:52706600-52732800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:52706600-52732800	Weak transcription	Pancreas	Pancrea
20	chr13:52707400-52731200	Weak transcription	Primary B cells from cord blood	blood
21	chr13:52707400-52732800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr13:52707600-52731600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr13:52707600-52732600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr13:52707800-52732600	Weak transcription	A549	lung
25	chr13:52708000-52732600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr13:52708400-52732600	Weak transcription	HSMMtube	muscle
27	chr13:52708400-52732800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr13:52710400-52732800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr13:52712200-52733000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr13:52712400-52733000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr13:52720800-52728600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr13:52720800-52732400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr13:52721800-52732600	Weak transcription	NHEK	skin
34	chr13:52723000-52732600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr13:52723000-52732600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr13:52724000-52731000	Weak transcription	Fetal Intestine Small	intestine
37	chr13:52724200-52732800	Weak transcription	Thymus	Thymus
38	chr13:52725400-52732600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr13:52725600-52728800	Weak transcription	Small Intestine	intestine
40	chr13:52725600-52731200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr13:52725800-52731000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr13:52725800-52732600	Weak transcription	Brain Germinal Matrix	brain
43	chr13:52725800-52732600	Weak transcription	Fetal Brain Female	brain
44	chr13:52725800-52732800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr13:52725800-52732800	Weak transcription	Ovary	ovary
46	chr13:52726000-52728800	Weak transcription	Fetal Stomach	stomach
47	chr13:52726000-52729400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr13:52726000-52730400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr13:52726000-52730400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr13:52726000-52730400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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