Variant report

Variant	rs1654774
Chromosome Location	chr6:28096280-28096281
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28072796..28075387-chr6:28095316..28098001,2	K562	blood:
2	chr6:28091137..28098786-chr6:28103559..28111884,14	MCF-7	breast:
3	chr6:28046111..28048022-chr6:28095723..28098620,2	K562	blood:
4	chr6:28089970..28093154-chr6:28093915..28098032,5	K562	blood:
5	chr6:28078707..28081490-chr6:28095158..28097725,2	K562	blood:
6	chr6:27868230..27870687-chr6:28094988..28097736,2	K562	blood:

Variant related genes	Relation type
ENSG00000269293	Chromatin interaction
ENSG00000196812	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000261839	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 29 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1150668	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1150670	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1150679	0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1150686	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1150690	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1150694	0.83[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1150705	0.86[JPT][hapmap]
rs1150707	0.81[ASW][hapmap];0.89[CEU][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs1150709	0.89[CEU][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes]
rs1150711	0.84[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs1150716	0.84[AMR][1000 genomes]
rs1150724	0.81[MKK][hapmap]
rs1150726	0.82[CHD][hapmap];0.86[JPT][hapmap];0.81[MKK][hapmap]
rs12214383	0.81[ASW][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.81[MKK][hapmap]
rs1225618	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1225710	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1225715	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1233713	0.89[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes]
rs12530158	0.86[JPT][hapmap]
rs13408	0.81[ASW][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap]
rs149956	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs149963	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs149971	0.81[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs149976	0.81[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap]
rs1531681	0.81[ASW][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.81[MKK][hapmap]
rs1736891	0.81[ASW][hapmap];0.89[CEU][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs1736895	0.81[ASW][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.81[MKK][hapmap]
rs1778484	0.82[CHD][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap]
rs1997660	0.88[MEX][hapmap];0.81[MKK][hapmap]
rs2021826	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs203869	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs203878	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2142730	0.89[CEU][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes]
rs2394049	0.86[JPT][hapmap]
rs2622320	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2622322	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2791333	0.92[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs707907	0.88[MEX][hapmap];0.81[MKK][hapmap]
rs7206	0.89[CEU][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs853683	0.88[MEX][hapmap];0.81[MKK][hapmap]
rs853684	0.81[ASW][hapmap];0.89[CEU][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes]
rs853690	0.88[MEX][hapmap];0.81[MKK][hapmap]
rs853693	0.88[MEX][hapmap];0.81[MKK][hapmap]
rs9301	0.84[CEU][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes]
rs9468333	0.88[MEX][hapmap];0.81[MKK][hapmap]

mRNA abundance (count:29)

SNP	Gene	Cis/trans	Tissue	Source
rs1654774	AL022393.7	cis	Heart Left Ventricle	GTEx
rs1654774	ZKSCAN3	cis	parietal	SCAN
rs1654774	ZNF187	cis	cerebellum	SCAN
rs1654774	ZKSCAN3	cis	cerebellum	SCAN
rs1654774	AL022393.7	cis	Nerve Tibial	GTEx
rs1654774	NKAPL	cis	parietal	SCAN
rs1654774	ZSCAN31	cis	lung	GTEx
rs1654774	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs1654774	ZSCAN31	cis	Esophagus Muscularis	GTEx
rs1654774	BTN3A3	cis	parietal	SCAN
rs1654774	ZSCAN31	cis	Thyroid	GTEx
rs1654774	ZNF323	cis	parietal	SCAN
rs1654774	AL022393.7	cis	Artery Tibial	GTEx
rs1654774	ZSCAN23	cis	parietal	SCAN
rs1654774	AL022393.7	cis	Muscle Skeletal	GTEx
rs1654774	RP5-874C20.3	cis	Thyroid	GTEx
rs1654774	AL022393.7	cis	Esophagus Muscularis	GTEx
rs1654774	ZSCAN23	cis	cerebellum	SCAN
rs1654774	ZNF323	cis	Cerebellum	GTEx
rs1654774	AL022393.7	cis	Artery Aorta	GTEx
rs1654774	ZNF389	cis	brain	BrainEAC
rs1654774	ZNF323	cis	Frontal Cortex	GTEx
rs1654774	ZNF323	cis	cerebellum	SCAN
rs1654774	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs1654774	ZNF323	cis	Temporal Cortex	GTEx
rs1654774	ZSCAN23	cis	Muscle Skeletal	GTEx
rs1654774	AL022393.7	cis	lung	GTEx
rs1654774	ZNF192	cis	cerebellum	SCAN
rs1654774	ZSCAN23	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28091200-28096600	Strong transcription	K562	blood
2	chr6:28092800-28101800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:28092800-28103800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:28092800-28103800	Weak transcription	Ovary	ovary
5	chr6:28092800-28104000	Weak transcription	Aorta	Aorta
6	chr6:28092800-28104000	Weak transcription	Small Intestine	intestine
7	chr6:28092800-28104200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:28093000-28096600	Weak transcription	NH-A	brain
9	chr6:28093000-28100200	Weak transcription	Brain Anterior Caudate	brain
10	chr6:28093000-28100800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr6:28093000-28103200	Weak transcription	NHLF	lung
12	chr6:28093000-28103800	Weak transcription	Psoas Muscle	Psoas
13	chr6:28093000-28104000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:28093000-28104200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:28093200-28097600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr6:28093200-28102400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:28093200-28103200	Weak transcription	HMEC	breast
18	chr6:28093200-28103600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:28093400-28096400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:28093400-28096400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr6:28093400-28098200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr6:28093400-28100600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:28093400-28102600	Weak transcription	NHDF-Ad	bronchial
24	chr6:28093400-28103200	Weak transcription	NHEK	skin
25	chr6:28093400-28103400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr6:28093600-28096800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:28093600-28096800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:28093600-28097600	Strong transcription	Stomach Smooth Muscle	stomach
29	chr6:28093600-28098000	Weak transcription	Brain Angular Gyrus	brain
30	chr6:28093600-28098600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:28093600-28098600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr6:28093600-28099200	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr6:28093600-28100200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:28093600-28101200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr6:28093600-28101200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:28093600-28101400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr6:28093600-28102200	Weak transcription	Brain Substantia Nigra	brain
38	chr6:28093600-28102600	Weak transcription	Right Ventricle	heart
39	chr6:28093600-28103200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:28093600-28103200	Weak transcription	Right Atrium	heart
41	chr6:28093600-28104000	Weak transcription	Fetal Intestine Small	intestine
42	chr6:28093600-28104200	Weak transcription	Pancreas	Pancrea
43	chr6:28093600-28104400	Weak transcription	Esophagus	oesophagus
44	chr6:28093600-28104400	Weak transcription	Gastric	stomach
45	chr6:28093800-28096800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr6:28093800-28097200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr6:28093800-28099600	Strong transcription	Fetal Thymus	thymus
48	chr6:28093800-28100600	Strong transcription	Primary B cells from peripheral blood	blood
49	chr6:28093800-28101400	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr6:28093800-28101600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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