Variant report

Variant	rs13193272
Chromosome Location	chr6:28392743-28392744
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28390398..28392930-chr6:28395199..28398373,4	K562	blood:
2	chr6:28389572..28392930-chr6:28395042..28397704,3	K562	blood:
3	chr6:28380846..28382983-chr6:28391973..28394917,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZSCAN23-1	chr6:28392120-28394123	NONHSAT108462

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1005126	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10807030	0.82[ASN][1000 genomes]
rs10807031	0.82[ASN][1000 genomes]
rs11751928	0.86[ASN][1000 genomes]
rs13190937	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13196606	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13199081	0.96[EUR][1000 genomes]
rs13203055	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13209596	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13215804	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13217326	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16894091	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16894106	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108923	0.82[ASN][1000 genomes]
rs2232427	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28505234	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs35908902	0.82[ASN][1000 genomes]
rs3799499	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3799500	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs57071502	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58020991	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6902687	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6905380	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6931359	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6940744	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71559081	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750526	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7754960	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7774981	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9468356	0.86[ASN][1000 genomes]
rs9468358	0.86[ASN][1000 genomes]
rs9969098	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	esv1836974	chr6:28376981-28398748	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13193272	ZSCAN23	cis	Artery Tibial	GTEx
rs13193272	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs13193272	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs13193272	AL022393.7	cis	Muscle Skeletal	GTEx
rs13193272	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs13193272	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28371200-28410400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:28383800-28393000	Weak transcription	Fetal Intestine Small	intestine
3	chr6:28384600-28410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:28385400-28402000	Weak transcription	Fetal Kidney	kidney
5	chr6:28385400-28402200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:28385600-28410800	Weak transcription	Lung	lung
7	chr6:28386000-28402200	Weak transcription	Osteobl	bone
8	chr6:28386000-28410400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:28386200-28395800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:28386600-28392800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:28386600-28397800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:28386800-28393600	Weak transcription	Fetal Heart	heart
13	chr6:28386800-28402200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr6:28387600-28393000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:28387600-28394200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:28387800-28393000	Weak transcription	Fetal Brain Male	brain
17	chr6:28387800-28395400	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:28387800-28410200	Weak transcription	Brain Angular Gyrus	brain
19	chr6:28388000-28392800	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr6:28388000-28410400	Weak transcription	NHDF-Ad	bronchial
21	chr6:28388400-28393000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:28388400-28399200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr6:28389200-28393200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:28389200-28410200	Weak transcription	NHLF	lung
25	chr6:28389400-28393000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:28389400-28403200	Weak transcription	Adipose Nuclei	Adipose
27	chr6:28389400-28410000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:28389600-28398200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:28389600-28409800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr6:28389600-28410200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr6:28389600-28410400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:28389600-28410400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:28389800-28392800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:28389800-28393000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr6:28389800-28410800	Weak transcription	Colonic Mucosa	Colon
36	chr6:28390000-28393200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:28390200-28410400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr6:28391000-28393000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr6:28391000-28395200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:28391400-28392800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr6:28391400-28402400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr6:28391400-28410400	Weak transcription	Fetal Intestine Large	intestine
43	chr6:28391400-28410800	Weak transcription	Placenta	Placenta
44	chr6:28391600-28392800	Weak transcription	Fetal Muscle Leg	muscle
45	chr6:28391600-28393000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr6:28391600-28393000	Weak transcription	Aorta	Aorta
47	chr6:28391600-28393000	Weak transcription	Fetal Stomach	stomach
48	chr6:28391600-28393000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr6:28391600-28393200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:28391600-28393200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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