Variant report

Variant	rs1233660
Chromosome Location	chr6:28260249-28260250
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28259497..28262038-chr6:28302378..28305573,5	K562	blood:

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs1150694	0.82[AFR][1000 genomes]
rs1150705	0.81[ASN][1000 genomes]
rs1150707	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1150709	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1150711	0.83[ASN][1000 genomes]
rs1150716	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1150718	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1150721	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1150724	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1150726	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12214383	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1225710	0.86[AFR][1000 genomes]
rs1233713	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13408	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1531681	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1736891	0.86[AFR][1000 genomes]
rs1736895	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1778484	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1997660	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2021826	0.82[AFR][1000 genomes]
rs213238	0.83[ASN][1000 genomes]
rs213240	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2142730	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2394049	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2622322	0.86[AFR][1000 genomes]
rs2791333	0.86[AFR][1000 genomes]
rs4713158	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707907	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7206	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs853683	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs853684	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs853690	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs853693	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9301	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9468333	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[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	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1233660	ZSCAN31	cis	Thyroid	GTEx
rs1233660	RP5-874C20.3	cis	Thyroid	GTEx
rs1233660	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs1233660	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs1233660	ZSCAN23	cis	Artery Tibial	GTEx
rs1233660	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs1233660	ZSCAN31	cis	lung	GTEx
rs1233660	AL022393.7	cis	Muscle Skeletal	GTEx
rs1233660	AL022393.7	cis	Nerve Tibial	GTEx
rs1233660	AL022393.7	cis	Heart Left Ventricle	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28249800-28272200	Weak transcription	Spleen	Spleen
2	chr6:28250000-28277600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:28250000-28293800	Weak transcription	Gastric	stomach
4	chr6:28250200-28273800	Weak transcription	Thymus	Thymus
5	chr6:28250400-28265600	Weak transcription	Primary T cells from cord blood	blood
6	chr6:28250400-28278600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr6:28250600-28267000	Weak transcription	NHEK	skin
8	chr6:28250600-28270800	Weak transcription	Fetal Heart	heart
9	chr6:28250600-28280600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:28250800-28270000	Weak transcription	Psoas Muscle	Psoas
11	chr6:28250800-28276800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:28251000-28270800	Weak transcription	Colonic Mucosa	Colon
13	chr6:28251000-28273800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:28251000-28277200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:28251000-28278800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:28251400-28262200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:28253400-28264400	Weak transcription	NHLF	lung
18	chr6:28253400-28264600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:28255200-28264400	Weak transcription	Aorta	Aorta
20	chr6:28255200-28268600	Weak transcription	Ovary	ovary
21	chr6:28255200-28271200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:28255200-28271600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:28255200-28278600	Weak transcription	Esophagus	oesophagus
24	chr6:28255200-28278600	Weak transcription	Pancreas	Pancrea
25	chr6:28255200-28278800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:28255200-28283000	Weak transcription	HSMMtube	muscle
27	chr6:28255200-28293800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr6:28255400-28261200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:28255400-28271200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr6:28255400-28278400	Weak transcription	HepG2	liver
31	chr6:28255600-28264800	Weak transcription	HUVEC	blood vessel
32	chr6:28255600-28271400	Weak transcription	Placenta	Placenta
33	chr6:28255600-28272000	Weak transcription	Brain Substantia Nigra	brain
34	chr6:28256000-28267600	Weak transcription	Osteobl	bone
35	chr6:28256200-28264400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr6:28256200-28264400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr6:28256400-28264800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr6:28256400-28268400	Weak transcription	Fetal Intestine Large	intestine
39	chr6:28256400-28271600	Weak transcription	Liver	Liver
40	chr6:28256400-28277800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr6:28256600-28264400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:28256600-28264400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr6:28256600-28264400	Weak transcription	Fetal Intestine Small	intestine
44	chr6:28256600-28264600	Weak transcription	Fetal Lung	lung
45	chr6:28256600-28268200	Weak transcription	Lung	lung
46	chr6:28256600-28268600	Weak transcription	Fetal Thymus	thymus
47	chr6:28256600-28280800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr6:28257400-28261800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:28257400-28264600	Weak transcription	Adipose Nuclei	Adipose
50	chr6:28257600-28261200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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