Variant report

Variant	rs1150726
Chromosome Location	chr6:28243042-28243043
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28239901..28245005-chr6:28300469..28305210,5	K562	blood:
2	chr6:28241790..28245187-chr6:28314070..28316476,3	K562	blood:
3	chr6:28241790..28244617-chr6:28314645..28316476,2	K562	blood:
4	chr6:28241961..28244891-chr6:28302513..28304698,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PGBD1-1	chr6:28242258-28243311	NONHSAT108451

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1005125	1.00[YRI][hapmap]
rs1052215	0.91[ASW][hapmap];0.95[CHB][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs1150668	0.90[JPT][hapmap]
rs1150694	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs1150705	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1150707	0.91[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs1150709	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs1150711	0.83[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.96[ASN][1000 genomes]
rs1150716	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1150718	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1150721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1150724	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12214383	0.91[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1225618	0.84[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs1225710	0.91[ASW][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs1225715	0.85[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap]
rs1233660	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1233713	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]
rs13408	0.91[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1531681	0.91[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1654774	0.82[CHD][hapmap];0.86[JPT][hapmap];0.81[MKK][hapmap]
rs1736891	0.91[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs1736895	0.91[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1778484	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1997660	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2021826	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs203878	0.91[ASW][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs213238	0.86[JPT][hapmap]
rs213240	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap]
rs2142730	1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2394049	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2622320	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2622322	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2791333	0.81[ASW][hapmap];0.81[CHD][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap]
rs2859348	0.91[CHB][hapmap]
rs4713158	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs707907	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7206	0.82[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs853683	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs853684	0.91[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs853690	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs853693	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9301	0.90[ASW][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.83[ASN][1000 genomes]
rs9468333	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[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
rs1150726	ZSCAN23	cis	parietal	SCAN
rs1150726	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs1150726	AL022393.7	cis	Muscle Skeletal	GTEx
rs1150726	AL022393.7	cis	Nerve Tibial	GTEx
rs1150726	ZSCAN31	cis	lung	GTEx
rs1150726	ZSCAN31	cis	Thyroid	GTEx
rs1150726	ZNF187	cis	cerebellum	SCAN
rs1150726	ZSCAN23	cis	cerebellum	SCAN
rs1150726	AL022393.7	cis	Heart Left Ventricle	GTEx
rs1150726	ZNF192	cis	cerebellum	SCAN
rs1150726	NKAPL	cis	parietal	SCAN
rs1150726	ZKSCAN3	cis	parietal	SCAN
rs1150726	GRIN3A	trans	cerebellum	SCAN
rs1150726	RP5-874C20.3	cis	Thyroid	GTEx
rs1150726	ZNF323	cis	cerebellum	SCAN
rs1150726	ZKSCAN3	cis	cerebellum	SCAN
rs1150726	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs1150726	HIST1H1D	cis	parietal	SCAN
rs1150726	BTN3A1	cis	parietal	SCAN
rs1150726	HIST1H4C	cis	parietal	SCAN
rs1150726	ZNF323	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28235400-28249000	Weak transcription	Small Intestine	intestine
2	chr6:28235600-28243400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:28235600-28249000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:28235600-28249000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:28236200-28247400	Weak transcription	Stomach Mucosa	stomach
6	chr6:28236200-28248000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:28236200-28249400	Weak transcription	Fetal Heart	heart
8	chr6:28237400-28245800	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr6:28237400-28249000	Weak transcription	Psoas Muscle	Psoas
10	chr6:28237600-28248800	Weak transcription	A549	lung
11	chr6:28238000-28245600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:28238000-28248800	Weak transcription	Hela-S3	cervix
13	chr6:28238200-28245200	Strong transcription	Fetal Intestine Large	intestine
14	chr6:28238800-28244000	Strong transcription	Ovary	ovary
15	chr6:28238800-28245400	Strong transcription	Fetal Stomach	stomach
16	chr6:28238800-28245600	Strong transcription	Primary T cells from cord blood	blood
17	chr6:28238800-28245800	Strong transcription	Fetal Muscle Trunk	muscle
18	chr6:28238800-28245800	Strong transcription	Stomach Smooth Muscle	stomach
19	chr6:28238800-28246000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:28239200-28243800	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr6:28239200-28244800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:28239200-28245000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:28239200-28245000	Strong transcription	Spleen	Spleen
24	chr6:28239200-28245200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr6:28239200-28245200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:28239200-28245200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:28239200-28245200	Strong transcription	Lung	lung
28	chr6:28239200-28245400	Strong transcription	Brain Anterior Caudate	brain
29	chr6:28239200-28245400	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr6:28239200-28245600	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:28239200-28245600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:28239200-28246000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:28239200-28246000	Strong transcription	Colon Smooth Muscle	Colon
34	chr6:28239400-28245000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:28239400-28245400	Strong transcription	Primary hematopoietic stem cells	blood
36	chr6:28239400-28246000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr6:28239600-28244800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr6:28239600-28244800	Strong transcription	Dnd41	blood
39	chr6:28239600-28245000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:28239600-28245000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:28239600-28245000	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr6:28239600-28245200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr6:28239600-28245200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr6:28239600-28245200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:28239600-28245200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:28239600-28245200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr6:28239600-28245200	Strong transcription	Adipose Nuclei	Adipose
48	chr6:28239600-28245200	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr6:28239600-28245200	Strong transcription	Brain Substantia Nigra	brain
50	chr6:28239600-28245200	Strong transcription	Placenta	Placenta

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