Variant report

Variant	rs1054372
Chromosome Location	chr6:28336742-28336743
allele	G/T
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:1)
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	chr6:28326753..28329477-chr6:28335475..28338195,2	K562	blood:
2	chr6:28336184..28339998-chr6:28343727..28348047,5	K562	blood:
3	chr6:28318727..28321441-chr6:28336675..28338219,2	K562	blood:
4	chr6:28335113..28339342-chr6:28340295..28342925,4	K562	blood:
5	chr6:28335113..28339342-chr6:28340295..28342683,4	K562	blood:
6	chr6:28331703..28333940-chr6:28336261..28337790,2	MCF-7	breast:
7	chr6:28303740..28306465-chr6:28335906..28338559,3	MCF-7	breast:
8	chr6:28304066..28305793-chr6:28336163..28337903,2	K562	blood:
9	chr6:28336184..28339617-chr6:28343727..28347086,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZKSCAN3-1	chr6:28336039-28336930	NONHSAT108460

No data

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1005127	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1124131	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11751693	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11752496	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11752919	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11754208	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755942	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11760133	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12697938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13201726	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13201753	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs13207208	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.95[ASN][1000 genomes]
rs13210866	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13215476	0.93[ASN][1000 genomes]
rs1339898	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13437294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1361385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1416918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1558205	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1591913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16894021	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16894060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16894095	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16894108	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1997660	0.83[CEU][hapmap]
rs2027361	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2041230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs213228	0.91[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2531804	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs28360638	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34513104	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34924864	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35191424	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35560946	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35599905	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36018474	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3734563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4254981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4357130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4580862	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4642462	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66542396	0.88[ASN][1000 genomes]
rs67211468	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6899389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6899603	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6903535	0.89[ASN][1000 genomes]
rs6907950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6908137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6917130	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6922169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6922374	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6922429	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6927229	0.89[ASN][1000 genomes]
rs6928773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6929825	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6939966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[ASN][1000 genomes]
rs707907	0.83[CEU][hapmap]
rs740621	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs740622	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7451726	0.84[ASN][1000 genomes]
rs7740351	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7749736	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764737	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773051	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775132	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853683	0.83[CEU][hapmap]
rs853690	0.83[CEU][hapmap]
rs853693	0.83[CEU][hapmap]
rs9461455	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9461456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461459	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468333	0.83[CEU][hapmap]
rs9468354	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468360	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9468361	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468365	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468366	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9468367	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1054372	ZSCAN31	cis	lung	GTEx
rs1054372	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs1054372	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs1054372	ZSCAN31	cis	Nerve Tibial	GTEx
rs1054372	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs1054372	AL022393.7	cis	Heart Left Ventricle	GTEx
rs1054372	ZSCAN31	cis	Thyroid	GTEx
rs1054372	RP5-874C20.3	cis	Thyroid	GTEx
rs1054372	AL022393.7	cis	Muscle Skeletal	GTEx
rs1054372	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28318400-28350800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:28324400-28347600	Weak transcription	NHDF-Ad	bronchial
3	chr6:28324400-28347800	Weak transcription	Fetal Brain Male	brain
4	chr6:28324400-28348200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr6:28324400-28357200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:28324400-28357600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:28324600-28349400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:28324600-28349600	Weak transcription	NHEK	skin
9	chr6:28324600-28358600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr6:28324800-28341600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr6:28325400-28350800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:28327000-28337600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:28327200-28338400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:28328000-28337000	Strong transcription	Liver	Liver
15	chr6:28328200-28336800	Strong transcription	Fetal Muscle Leg	muscle
16	chr6:28330800-28337600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:28330800-28338600	Strong transcription	Primary T cells from cord blood	blood
18	chr6:28331200-28337600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:28332000-28350600	Weak transcription	Psoas Muscle	Psoas
20	chr6:28333800-28345800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:28333800-28347800	Weak transcription	HUVEC	blood vessel
22	chr6:28333800-28348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:28333800-28349800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:28333800-28349800	Weak transcription	Pancreas	Pancrea
25	chr6:28333800-28350800	Weak transcription	Lung	lung
26	chr6:28333800-28351000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr6:28334000-28338200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:28334000-28338400	Weak transcription	Fetal Brain Female	brain
29	chr6:28334000-28345600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:28334000-28346600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:28334000-28346800	Weak transcription	Fetal Kidney	kidney
32	chr6:28334000-28348000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr6:28334000-28350000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr6:28334000-28350600	Weak transcription	Colonic Mucosa	Colon
35	chr6:28334000-28350800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:28334200-28345200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr6:28334200-28345600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:28334200-28345600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:28334200-28346000	Weak transcription	Fetal Intestine Small	intestine
40	chr6:28334200-28346000	Weak transcription	HMEC	breast
41	chr6:28334200-28346200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:28334200-28347800	Weak transcription	NHLF	lung
43	chr6:28334200-28348000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr6:28334200-28348000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr6:28334200-28348200	Weak transcription	Brain Substantia Nigra	brain
46	chr6:28334200-28348800	Weak transcription	Fetal Heart	heart
47	chr6:28334200-28349400	Weak transcription	Right Ventricle	heart
48	chr6:28334200-28349800	Weak transcription	Aorta	Aorta
49	chr6:28334200-28351000	Weak transcription	Gastric	stomach
50	chr6:28334200-28351200	Weak transcription	Spleen	Spleen

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