Variant report

Variant	rs1233713
Chromosome Location	chr6:28198281-28198282
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28109641..28111388-chr6:28197093..28199028,2	K562	blood:
2	chr6:28196925..28198715-chr6:28230690..28232627,2	K562	blood:
3	chr6:28197985..28199991-chr6:28239613..28241567,2	K562	blood:
4	chr6:28186179..28187868-chr6:28196077..28199044,2	MCF-7	breast:
5	chr6:28107272..28109222-chr6:28196565..28198817,2	K562	blood:
6	chr6:28198039..28200844-chr6:28211243..28213952,3	MCF-7	breast:
7	chr6:28195857..28199662-chr6:28302729..28304554,3	K562	blood:
8	chr6:28198177..28200363-chr6:28214686..28217029,3	MCF-7	breast:
9	chr6:28197104..28198683-chr6:28303467..28305240,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000198315	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000176933	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1005125	0.87[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs1052215	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs1124132	0.82[EUR][1000 genomes]
rs1150668	0.89[CEU][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes]
rs1150670	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1150679	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1150686	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1150690	0.87[AMR][1000 genomes]
rs1150694	0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1150705	0.96[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1150707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1150716	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1150718	0.96[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs1150721	0.96[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1150724	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1150726	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12214383	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1225618	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1225710	0.96[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1225715	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1233660	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13408	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs149956	0.92[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs1531681	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1654774	0.89[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes]
rs1736891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1736895	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1736904	0.84[CHB][hapmap]
rs1778484	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1997660	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2021826	0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2023493	0.82[EUR][1000 genomes]
rs203869	0.96[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs203878	0.96[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs213236	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs213237	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs213238	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs213240	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2142730	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2247002	0.81[EUR][1000 genomes]
rs2394049	0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2531825	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2531831	0.81[EUR][1000 genomes]
rs2531832	0.82[EUR][1000 genomes]
rs2622320	0.96[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2622322	0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2791333	0.96[CEU][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2859348	0.82[CEU][hapmap];0.87[CHB][hapmap]
rs2859365	0.81[EUR][1000 genomes]
rs34024998	0.92[EUR][1000 genomes]
rs4713158	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs707907	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7206	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728122	0.81[EUR][1000 genomes]
rs853683	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs853684	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs853690	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs853693	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9301	0.96[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9368565	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9468333	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[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:26)

SNP	Gene	Cis/trans	Tissue	Source
rs1233713	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs1233713	ZSCAN31	cis	Muscle Skeletal	GTEx
rs1233713	ZSCAN31	cis	lung	GTEx
rs1233713	ZSCAN23	cis	Artery Tibial	GTEx
rs1233713	AL022393.7	cis	Esophagus Muscularis	GTEx
rs1233713	ZNF323	cis	Cerebellum	GTEx
rs1233713	AL022393.7	cis	Nerve Tibial	GTEx
rs1233713	RP5-874C20.3	cis	Thyroid	GTEx
rs1233713	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs1233713	ZNF323	cis	Frontal Cortex	GTEx
rs1233713	ZSCAN23	cis	lung	GTEx
rs1233713	AL022393.7	cis	Artery Aorta	GTEx
rs1233713	ZSCAN23	cis	Adipose Subcutaneous	GTEx
rs1233713	ZSCAN31	cis	Stomach	GTEx
rs1233713	ZSCAN31	cis	Thyroid	GTEx
rs1233713	ZSCAN31	cis	Esophagus Muscularis	GTEx
rs1233713	AL022393.7	cis	lung	GTEx
rs1233713	ZSCAN23	cis	Muscle Skeletal	GTEx
rs1233713	TRIM27	cis	Skin Sun Exposed Lower leg	GTEx
rs1233713	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs1233713	ZNF323	cis	Temporal Cortex	GTEx
rs1233713	AL022393.7	cis	Heart Left Ventricle	GTEx
rs1233713	AL022393.7	cis	Artery Tibial	GTEx
rs1233713	ZNF323	cis	Brain Pons	GTEx
rs1233713	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs1233713	AL022393.7	cis	Muscle Skeletal	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28193600-28213400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:28193800-28204000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:28193800-28211800	Weak transcription	Fetal Thymus	thymus
4	chr6:28193800-28218400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:28193800-28218400	Weak transcription	Stomach Mucosa	stomach
6	chr6:28194000-28211000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr6:28194000-28211800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:28194000-28212800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:28194000-28213000	Weak transcription	Thymus	Thymus
10	chr6:28194000-28213600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:28194600-28199800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:28194600-28207000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:28194800-28199000	Strong transcription	HSMMtube	muscle
14	chr6:28194800-28202800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:28194800-28202800	Strong transcription	Fetal Muscle Trunk	muscle
16	chr6:28194800-28202800	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr6:28194800-28204200	Strong transcription	Left Ventricle	heart
18	chr6:28194800-28205000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:28195000-28198800	Strong transcription	Hela-S3	cervix
20	chr6:28195000-28199000	Strong transcription	HSMM	muscle
21	chr6:28195000-28199000	Strong transcription	Osteobl	bone
22	chr6:28195000-28199400	Strong transcription	Primary hematopoietic stem cells	blood
23	chr6:28195000-28199400	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr6:28195000-28199600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:28195000-28200000	Strong transcription	NH-A	brain
26	chr6:28195000-28200200	Strong transcription	HUVEC	blood vessel
27	chr6:28195000-28201200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:28195000-28201200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:28195000-28201200	Strong transcription	Ovary	ovary
30	chr6:28195000-28201400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:28195000-28201600	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr6:28195000-28201600	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr6:28195000-28201600	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr6:28195000-28201600	Strong transcription	HepG2	liver
35	chr6:28195000-28202000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr6:28195000-28202000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:28195000-28202000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:28195000-28202000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:28195000-28202000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr6:28195000-28202200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:28195000-28202200	Strong transcription	Duodenum Mucosa	Duodenum
42	chr6:28195000-28202200	Strong transcription	Fetal Lung	lung
43	chr6:28195000-28202400	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr6:28195000-28202600	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr6:28195000-28202600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:28195000-28202600	Strong transcription	Fetal Stomach	stomach
47	chr6:28195000-28202600	Strong transcription	NHLF	lung
48	chr6:28195000-28202800	Strong transcription	Liver	Liver
49	chr6:28195000-28203000	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr6:28195000-28203000	Strong transcription	Fetal Intestine Large	intestine

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