Variant report

Variant	rs13201753
Chromosome Location	chr6:28331128-28331129
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28329825..28331904-chr6:28351268..28353364,2	K562	blood:
2	chr6:28323337..28330678-chr6:28330738..28334657,8	K562	blood:
3	chr6:28329274..28332112-chr6:28332342..28334041,2	MCF-7	breast:
4	chr6:28325434..28327610-chr6:28328938..28331453,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs1054372	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs11752496	0.81[AMR][1000 genomes]
rs11752919	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs11755942	0.94[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs12697938	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs13207208	1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap]
rs13437294	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs1361385	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs1416918	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs1558205	0.89[CEU][hapmap];0.87[JPT][hapmap]
rs1591913	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs16894060	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs2041230	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs2071965	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs213228	0.94[CEU][hapmap];0.87[JPT][hapmap]
rs213230	0.88[CEU][hapmap]
rs2531804	0.87[JPT][hapmap]
rs34924864	0.81[AMR][1000 genomes]
rs35191424	0.82[AMR][1000 genomes]
rs3734563	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs3800328	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs4254981	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs4357130	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs6899389	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6907950	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs6908137	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs6917130	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6922169	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6922374	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes]
rs6928773	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6939966	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[YRI][hapmap]
rs7759191	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs7764722	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs9461455	0.82[AMR][1000 genomes]
rs9461456	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs9461458	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs9461459	0.94[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs9468354	0.80[AMR][1000 genomes]
rs9468355	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs9468357	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs9468368	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs9468370	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs13201753	RP5-874C20.3	cis	Thyroid	GTEx
rs13201753	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs13201753	AL022393.7	cis	Muscle Skeletal	GTEx
rs13201753	ZSCAN31	cis	Nerve Tibial	GTEx
rs13201753	ZSCAN31	cis	lung	GTEx
rs13201753	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs13201753	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs13201753	AL022393.7	cis	Heart Left Ventricle	GTEx
rs13201753	ZSCAN31	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28318400-28332000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:28318400-28350800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:28324200-28331600	Weak transcription	Thymus	Thymus
4	chr6:28324400-28331200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr6:28324400-28331600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:28324400-28332600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:28324400-28333000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr6:28324400-28333000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:28324400-28333200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:28324400-28336000	Weak transcription	GM12878-XiMat	blood
11	chr6:28324400-28347600	Weak transcription	NHDF-Ad	bronchial
12	chr6:28324400-28347800	Weak transcription	Fetal Brain Male	brain
13	chr6:28324400-28348200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr6:28324400-28357200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:28324400-28357600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr6:28324600-28331200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:28324600-28331200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:28324600-28331200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:28324600-28331200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr6:28324600-28331600	Weak transcription	Fetal Kidney	kidney
21	chr6:28324600-28331800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:28324600-28332000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:28324600-28332600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:28324600-28332600	Weak transcription	Brain Angular Gyrus	brain
25	chr6:28324600-28332600	Weak transcription	HSMM	muscle
26	chr6:28324600-28332800	Weak transcription	Fetal Heart	heart
27	chr6:28324600-28349400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:28324600-28349600	Weak transcription	NHEK	skin
29	chr6:28324600-28358600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr6:28324800-28331200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:28324800-28331800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:28324800-28332000	Weak transcription	Esophagus	oesophagus
33	chr6:28324800-28341600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr6:28325000-28331400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:28325000-28331800	Weak transcription	NHLF	lung
36	chr6:28325000-28332200	Weak transcription	HepG2	liver
37	chr6:28325000-28333200	Weak transcription	HMEC	breast
38	chr6:28325200-28331200	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr6:28325200-28331200	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr6:28325200-28331400	Weak transcription	Gastric	stomach
41	chr6:28325200-28331400	Weak transcription	Right Ventricle	heart
42	chr6:28325200-28331400	Weak transcription	A549	lung
43	chr6:28325200-28331600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr6:28325200-28333000	Weak transcription	Dnd41	blood
45	chr6:28325200-28333000	Weak transcription	NH-A	brain
46	chr6:28325400-28332800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr6:28325400-28350800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr6:28325600-28333200	Weak transcription	HUVEC	blood vessel
49	chr6:28326800-28332800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr6:28326800-28335400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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