Variant report

Variant	rs13199081
Chromosome Location	chr6:28331834-28331835
allele	C/T
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	chr6:28331703..28333940-chr6:28336261..28337790,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1005126	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11751487	0.83[ASN][1000 genomes]
rs11751928	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11755387	0.92[CHB][hapmap]
rs13190937	1.00[CHB][hapmap]
rs13193272	0.96[EUR][1000 genomes]
rs13196606	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13203055	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13209596	0.94[EUR][1000 genomes]
rs13215804	1.00[CHB][hapmap]
rs13217326	0.84[EUR][1000 genomes]
rs16894011	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs16894091	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16894106	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17856167	0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs2232427	0.83[CEU][hapmap];0.92[CHB][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28505234	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3799499	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3799500	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs57071502	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs58020991	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6902687	1.00[CHB][hapmap]
rs6905380	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6931359	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6940744	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71559081	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7740429	0.96[EUR][1000 genomes]
rs7750526	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7754960	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7766356	0.80[CEU][hapmap]
rs7774981	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9468356	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9468358	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9468364	0.91[CHB][hapmap]
rs9969098	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13199081	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs13199081	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs13199081	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs13199081	ZSCAN23	cis	Artery Tibial	GTEx
rs13199081	AL022393.7	cis	Heart Left Ventricle	GTEx
rs13199081	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs13199081	AL022393.7	cis	Muscle Skeletal	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	chr6:28324400-28332600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:28324400-28333000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr6:28324400-28333000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr6:28324400-28333200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:28324400-28336000	Weak transcription	GM12878-XiMat	blood
8	chr6:28324400-28347600	Weak transcription	NHDF-Ad	bronchial
9	chr6:28324400-28347800	Weak transcription	Fetal Brain Male	brain
10	chr6:28324400-28348200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:28324400-28357200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:28324400-28357600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:28324600-28332000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:28324600-28332600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:28324600-28332600	Weak transcription	Brain Angular Gyrus	brain
16	chr6:28324600-28332600	Weak transcription	HSMM	muscle
17	chr6:28324600-28332800	Weak transcription	Fetal Heart	heart
18	chr6:28324600-28349400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:28324600-28349600	Weak transcription	NHEK	skin
20	chr6:28324600-28358600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr6:28324800-28332000	Weak transcription	Esophagus	oesophagus
22	chr6:28324800-28341600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr6:28325000-28332200	Weak transcription	HepG2	liver
24	chr6:28325000-28333200	Weak transcription	HMEC	breast
25	chr6:28325200-28333000	Weak transcription	Dnd41	blood
26	chr6:28325200-28333000	Weak transcription	NH-A	brain
27	chr6:28325400-28332800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr6:28325400-28350800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:28325600-28333200	Weak transcription	HUVEC	blood vessel
30	chr6:28326800-28332800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:28326800-28335400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:28326800-28336200	Strong transcription	Adipose Nuclei	Adipose
33	chr6:28327000-28334800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:28327000-28334800	Strong transcription	Placenta	Placenta
35	chr6:28327000-28336200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr6:28327000-28336200	Strong transcription	Fetal Stomach	stomach
37	chr6:28327000-28337600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:28327200-28334600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:28327200-28335400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr6:28327200-28338400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:28327400-28334200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr6:28327400-28334400	Strong transcription	Fetal Intestine Large	intestine
43	chr6:28327800-28335200	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr6:28327800-28335600	Strong transcription	K562	blood
45	chr6:28328000-28333000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr6:28328000-28334600	Strong transcription	Stomach Smooth Muscle	stomach
47	chr6:28328000-28337000	Strong transcription	Liver	Liver
48	chr6:28328200-28334200	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr6:28328200-28334400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:28328200-28334600	Strong transcription	Duodenum Smooth Muscle	Duodenum

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