Variant report

Variant	rs1150705
Chromosome Location	chr6:28193786-28193787
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr6:28192490-28194333	Hela-S3	cervix:	n/a	n/a
2	REST	chr6:28192080-28193913	H1-neurons	neurons:	n/a	n/a
3	TEAD4	chr6:28192337-28193881	K562	blood:	n/a	n/a
4	GABPA	chr6:28192364-28193830	MCF-7	breast:	n/a	n/a
5	SIN3A	chr6:28192820-28193830	H1-hESC	embryonic stem cell:	n/a	n/a
6	STAT3	chr6:28193518-28193814	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28184931..28189194-chr6:28190077..28194573,12	MCF-7	breast:
2	chr6:28182735..28195387-chr6:28315960..28325841,32	K562	blood:
3	chr6:28191649..28195458-chr6:28301378..28307708,9	K562	blood:
4	chr6:28191774..28193950-chr6:28248058..28250874,2	K562	blood:
5	chr6:28183629..28195178-chr6:28316250..28325659,29	K562	blood:
6	chr6:28103649..28105487-chr6:28192545..28194839,2	MCF-7	breast:
7	chr6:28102806..28106129-chr6:28190797..28194598,4	K562	blood:
8	chr6:28191711..28195552-chr6:28216768..28221883,5	MCF-7	breast:
9	chr6:28102723..28113786-chr6:28183725..28194756,41	K562	blood:
10	chr6:28184339..28187958-chr6:28190844..28194750,7	MCF-7	breast:
11	chr6:28191934..28194357-chr6:28233804..28235938,2	MCF-7	breast:
12	chr6:28191542..28194803-chr6:28365970..28368645,4	K562	blood:
13	chr6:27859047..27860986-chr6:28192686..28194393,2	K562	blood:
14	chr6:28192051..28194433-chr6:28219534..28221191,2	MCF-7	breast:
15	chr6:28191609..28196785-chr6:28301378..28305522,8	K562	blood:
16	chr6:28108436..28110620-chr6:28192837..28194996,3	MCF-7	breast:
17	chr6:28108043..28113786-chr6:28190485..28194607,10	K562	blood:
18	chr6:27798954..27801175-chr6:28191953..28194580,2	K562	blood:

No data

Variant related genes	Relation type
ZSCAN9	TF binding region
ENSG00000197153	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000197914	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000158691	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000269293	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1005125	0.81[EUR][1000 genomes]
rs1052215	0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs1124132	0.81[EUR][1000 genomes]
rs1150668	0.91[JPT][hapmap]
rs1150670	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1150679	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1150686	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1150694	0.91[JPT][hapmap];0.88[EUR][1000 genomes]
rs1150707	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1150709	0.96[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1150711	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1150716	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1150718	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs1150721	0.92[CHB][hapmap]
rs1150724	0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1150726	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12214383	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1225618	0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1225710	0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1225715	0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1233660	0.81[ASN][1000 genomes]
rs1233713	0.96[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13408	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs149956	0.81[JPT][hapmap]
rs1531681	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1654774	0.86[JPT][hapmap]
rs1736891	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1736895	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1778484	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1997660	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2021826	0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2023493	0.81[EUR][1000 genomes]
rs203869	0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs203878	0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs213236	0.82[EUR][1000 genomes]
rs213237	0.82[EUR][1000 genomes]
rs213238	0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs213240	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2142730	0.91[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2247002	0.81[EUR][1000 genomes]
rs2394049	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2531825	0.81[EUR][1000 genomes]
rs2531831	0.81[EUR][1000 genomes]
rs2531832	0.81[EUR][1000 genomes]
rs2622320	0.90[JPT][hapmap]
rs2622322	0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2791333	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2859348	0.83[CHB][hapmap]
rs2859365	0.81[EUR][1000 genomes]
rs34024998	0.92[EUR][1000 genomes]
rs4713158	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs707907	0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes]
rs7206	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs728122	0.81[EUR][1000 genomes]
rs853683	0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes]
rs853684	0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs853690	0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes]
rs853693	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes]
rs9301	0.86[CHB][hapmap];0.80[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9368565	0.82[EUR][1000 genomes]
rs9468333	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.81[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:21)

SNP	Gene	Cis/trans	Tissue	Source
rs1150705	ZSCAN31	cis	Esophagus Muscularis	GTEx
rs1150705	ZSCAN23	cis	Artery Tibial	GTEx
rs1150705	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs1150705	ZSCAN23	cis	lung	GTEx
rs1150705	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs1150705	ZSCAN31	cis	Thyroid	GTEx
rs1150705	AL022393.7	cis	Muscle Skeletal	GTEx
rs1150705	TRIM27	cis	Skin Sun Exposed Lower leg	GTEx
rs1150705	RP5-874C20.3	cis	Thyroid	GTEx
rs1150705	ZSCAN31	cis	lung	GTEx
rs1150705	AL022393.7	cis	Artery Tibial	GTEx
rs1150705	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs1150705	ZSCAN31	cis	Muscle Skeletal	GTEx
rs1150705	ZSCAN23	cis	Muscle Skeletal	GTEx
rs1150705	ZSCAN23	cis	Adipose Subcutaneous	GTEx
rs1150705	ZSCAN23	cis	Stomach	GTEx
rs1150705	AL022393.7	cis	Esophagus Muscularis	GTEx
rs1150705	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs1150705	AL022393.7	cis	Heart Left Ventricle	GTEx
rs1150705	AL022393.7	cis	lung	GTEx
rs1150705	AL022393.7	cis	Nerve Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28192400-28193800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr6:28192400-28194000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:28192400-28194000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:28192400-28194000	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr6:28192400-28194000	Active TSS	Fetal Kidney	kidney
6	chr6:28192400-28194000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr6:28192400-28194000	Active TSS	Rectal Smooth Muscle	rectum
8	chr6:28192400-28194000	Active TSS	Right Ventricle	heart
9	chr6:28192400-28194000	Active TSS	HSMM	muscle
10	chr6:28192400-28194200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:28192400-28194200	Active TSS	Psoas Muscle	Psoas
12	chr6:28192400-28194200	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr6:28192400-28194400	Active TSS	NHLF	lung
14	chr6:28192600-28193800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:28192600-28193800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
16	chr6:28192600-28193800	Active TSS	Fetal Heart	heart
17	chr6:28192600-28193800	Active TSS	Lung	lung
18	chr6:28192600-28193800	Active TSS	Placenta Amnion	Placenta Amnion
19	chr6:28192600-28193800	Bivalent/Poised TSS	HepG2	liver
20	chr6:28192600-28193800	Active TSS	NHDF-Ad	bronchial
21	chr6:28192600-28194000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:28192600-28194000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:28192600-28194000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:28192600-28194000	Active TSS	Fetal Intestine Large	intestine
25	chr6:28192600-28194000	Active TSS	Fetal Intestine Small	intestine
26	chr6:28192600-28194000	Active TSS	Fetal Muscle Trunk	muscle
27	chr6:28192600-28194200	Active TSS	H9 Cell Line	embryonic stem cell
28	chr6:28192600-28194200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:28192600-28194200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:28192600-28194200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:28192600-28194200	Active TSS	A549	lung
32	chr6:28192600-28194200	Active TSS	HSMMtube	muscle
33	chr6:28192600-28194400	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr6:28192600-28194400	Active TSS	H1 Cell Line	embryonic stem cell
35	chr6:28192600-28194400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:28192600-28194400	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr6:28192600-28194400	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr6:28192800-28193800	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr6:28192800-28193800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr6:28192800-28193800	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr6:28192800-28194000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr6:28192800-28194000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:28192800-28194000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:28192800-28194000	Active TSS	K562	blood
45	chr6:28192800-28194000	Active TSS	NHEK	skin
46	chr6:28192800-28194200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:28192800-28194200	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr6:28192800-28194200	Active TSS	Fetal Stomach	stomach
49	chr6:28192800-28194200	Active TSS	HMEC	breast
50	chr6:28192800-28194200	Active TSS	NH-A	brain

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