Variant report

Variant	rs1150724
Chromosome Location	chr6:28250236-28250237
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	chr6:28245880..28256877-chr6:28299741..28307557,21	K562	blood:
2	chr6:28247415..28251168-chr6:28301808..28306623,8	K562	blood:
3	chr6:28249255..28252885-chr6:28315781..28319284,4	K562	blood:
4	chr6:28186460..28191177-chr6:28246836..28252039,7	K562	blood:
5	chr6:28248171..28250694-chr6:28301952..28304469,4	MCF-7	breast:
6	chr6:28191774..28193950-chr6:28248058..28250874,2	K562	blood:
7	chr6:28232995..28235984-chr6:28248211..28251032,3	MCF-7	breast:
8	chr6:28247781..28251138-chr6:28322226..28325499,4	K562	blood:
9	chr6:28249727..28254264-chr6:28300327..28304071,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000189298	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000197062	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1005125	1.00[YRI][hapmap]
rs1052215	0.91[ASW][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs1150694	1.00[YRI][hapmap]
rs1150705	0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1150707	0.91[ASW][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs1150709	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs1150711	0.83[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.84[ASN][1000 genomes]
rs1150716	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1150718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1150721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1150726	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];0.82[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1225618	0.83[MEX][hapmap];0.83[TSI][hapmap]
rs1225710	0.91[ASW][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs1225715	0.83[TSI][hapmap]
rs1233660	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1233713	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]
rs13408	0.91[ASW][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.86[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];0.84[ASN][1000 genomes]
rs1531681	0.91[ASW][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1654774	0.81[MKK][hapmap]
rs1736891	0.91[ASW][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs1736895	0.91[ASW][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1778484	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1997660	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2021826	1.00[YRI][hapmap]
rs213237	0.81[CHD][hapmap]
rs213238	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs213240	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap];0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2142730	1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2394049	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2622320	1.00[YRI][hapmap]
rs2622322	1.00[YRI][hapmap]
rs2791333	0.81[ASW][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap]
rs2859348	0.91[CHB][hapmap]
rs4713158	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs707907	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7206	0.82[ASW][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs853683	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs853684	0.91[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs853690	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs853693	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9301	0.90[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9468333	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[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:23)

SNP	Gene	Cis/trans	Tissue	Source
rs1150724	ZKSCAN3	cis	cerebellum	SCAN
rs1150724	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs1150724	ZSCAN31	cis	lung	GTEx
rs1150724	ZNF187	cis	cerebellum	SCAN
rs1150724	ZSCAN23	cis	cerebellum	SCAN
rs1150724	ZNF192	cis	cerebellum	SCAN
rs1150724	AL022393.7	cis	Heart Left Ventricle	GTEx
rs1150724	AL022393.7	cis	Nerve Tibial	GTEx
rs1150724	BTN3A1	cis	parietal	SCAN
rs1150724	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs1150724	GRIN3A	trans	cerebellum	SCAN
rs1150724	ZKSCAN3	cis	parietal	SCAN
rs1150724	ZSCAN23	cis	parietal	SCAN
rs1150724	ZSCAN31	cis	Thyroid	GTEx
rs1150724	ZSCAN23	cis	Artery Tibial	GTEx
rs1150724	RP5-874C20.3	cis	Thyroid	GTEx
rs1150724	HIST1H1D	cis	parietal	SCAN
rs1150724	ZNF323	cis	cerebellum	SCAN
rs1150724	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs1150724	NKAPL	cis	parietal	SCAN
rs1150724	AL022393.7	cis	Muscle Skeletal	GTEx
rs1150724	ZNF323	cis	parietal	SCAN
rs1150724	HIST1H4C	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28248200-28251000	Active TSS	H1 Cell Line	embryonic stem cell
2	chr6:28248800-28250400	Active TSS	Stomach Smooth Muscle	stomach
3	chr6:28248800-28250400	Active TSS	K562	blood
4	chr6:28248800-28250400	Active TSS	NHLF	lung
5	chr6:28248800-28250600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:28248800-28250600	Active TSS	A549	lung
7	chr6:28248800-28250800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr6:28248800-28250800	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr6:28248800-28251000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:28249000-28250400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:28249000-28250400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:28249000-28250400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:28249000-28250400	Active TSS	Rectal Smooth Muscle	rectum
14	chr6:28249000-28250600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:28249000-28250600	Active TSS	Fetal Lung	lung
16	chr6:28249000-28250600	Active TSS	Right Atrium	heart
17	chr6:28249000-28250600	Active TSS	Right Ventricle	heart
18	chr6:28249000-28250800	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr6:28249000-28250800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:28249000-28250800	Active TSS	Psoas Muscle	Psoas
21	chr6:28249000-28251000	Active TSS	H9 Cell Line	embryonic stem cell
22	chr6:28249000-28251000	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr6:28249000-28251000	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr6:28249000-28251000	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr6:28249000-28251000	Active TSS	HSMM	muscle
26	chr6:28249200-28251200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:28249600-28250400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:28249600-28250400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:28249600-28250400	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr6:28249600-28250600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:28249800-28250400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:28249800-28250400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr6:28249800-28250400	Flanking Active TSS	Colon Smooth Muscle	Colon
34	chr6:28249800-28250400	Flanking Active TSS	HepG2	liver
35	chr6:28249800-28250600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr6:28249800-28250600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:28249800-28250600	Flanking Active TSS	Fetal Brain Female	brain
38	chr6:28249800-28250600	Flanking Active TSS	HUVEC	blood vessel
39	chr6:28249800-28251000	Flanking Active TSS	Dnd41	blood
40	chr6:28249800-28251600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:28249800-28272200	Weak transcription	Spleen	Spleen
42	chr6:28250000-28250400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr6:28250000-28250400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:28250000-28250400	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr6:28250000-28250400	Enhancers	Primary hematopoietic stem cells	blood
46	chr6:28250000-28250400	Flanking Active TSS	Fetal Kidney	kidney
47	chr6:28250000-28250400	Enhancers	HSMMtube	muscle
48	chr6:28250000-28250600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:28250000-28250600	Weak transcription	Liver	Liver
50	chr6:28250000-28250600	Enhancers	Fetal Thymus	thymus

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