Variant report

Variant	rs213228
Chromosome Location	chr6:28331252-28331253
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28329825..28331904-chr6:28351268..28353364,2	K562	blood:
2	chr6:28323337..28330678-chr6:28330738..28334657,8	K562	blood:
3	chr6:28329274..28332112-chr6:28332342..28334041,2	MCF-7	breast:
4	chr6:28325434..28327610-chr6:28328938..28331453,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1005127	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1054372	0.91[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1124131	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11751693	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11752496	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11752919	0.84[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs11754208	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11755942	0.91[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11760133	0.81[EUR][1000 genomes]
rs12697938	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13201726	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13201753	0.94[CEU][hapmap];0.87[JPT][hapmap]
rs13207208	1.00[JPT][hapmap]
rs13210866	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1339898	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13437294	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1361385	0.91[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1416918	0.91[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1558205	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1591913	0.91[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16894021	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16894060	0.91[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16894095	0.89[EUR][1000 genomes]
rs16894108	0.89[EUR][1000 genomes]
rs1997660	0.83[CEU][hapmap]
rs2027361	0.89[EUR][1000 genomes]
rs2041230	0.91[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2071965	0.91[CEU][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs213236	0.83[YRI][hapmap]
rs213237	0.83[YRI][hapmap]
rs2531804	1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[ASN][1000 genomes]
rs2531825	0.84[MKK][hapmap];0.83[YRI][hapmap]
rs28360638	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34513104	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34924864	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35191424	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35560946	0.89[EUR][1000 genomes]
rs35599905	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36018474	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3734563	0.91[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3800328	0.91[CEU][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs4254981	0.91[CEU][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4357130	0.91[CEU][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4580862	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4642462	0.89[EUR][1000 genomes]
rs67211468	0.89[EUR][1000 genomes]
rs6899389	0.91[CEU][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6899603	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6907950	0.91[CEU][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6908137	0.91[CEU][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6917130	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs6922169	0.91[CEU][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6922374	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs6922429	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6928773	0.91[CEU][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs6929825	0.89[EUR][1000 genomes]
rs6939966	1.00[JPT][hapmap]
rs707907	0.83[CEU][hapmap]
rs740621	0.89[EUR][1000 genomes]
rs740622	0.89[EUR][1000 genomes]
rs7740351	0.89[EUR][1000 genomes]
rs7749736	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7759191	0.91[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7764722	0.91[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7764737	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7773051	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7775132	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs853683	0.83[CEU][hapmap]
rs853690	0.83[CEU][hapmap]
rs853693	0.83[CEU][hapmap]
rs9461455	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9461456	0.91[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9461458	0.91[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9461459	0.87[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9468333	0.83[CEU][hapmap]
rs9468354	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9468355	0.91[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9468357	0.91[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9468360	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9468361	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9468365	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9468366	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9468367	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9468368	0.91[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9468370	0.91[CEU][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[EUR][1000 genomes];0.83[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:22)

SNP	Gene	Cis/trans	Tissue	Source
rs213228	ZNF192	cis	cerebellum	SCAN
rs213228	AL022393.7	cis	Muscle Skeletal	GTEx
rs213228	ZSCAN23	cis	Muscle Skeletal	GTEx
rs213228	ZSCAN23	cis	cerebellum	SCAN
rs213228	HIST1H2BN	cis	cerebellum	SCAN
rs213228	ZNF187	cis	cerebellum	SCAN
rs213228	RP5-874C20.3	cis	Thyroid	GTEx
rs213228	ZSCAN23	cis	parietal	SCAN
rs213228	ZSCAN31	cis	Thyroid	GTEx
rs213228	ZKSCAN3	cis	Skin Sun Exposed Lower leg	GTEx
rs213228	ZNF323	cis	parietal	SCAN
rs213228	AL022393.7	cis	Heart Left Ventricle	GTEx
rs213228	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs213228	ZSCAN31	cis	lung	GTEx
rs213228	AL022393.7	cis	Nerve Tibial	GTEx
rs213228	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs213228	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs213228	ZKSCAN3	cis	cerebellum	SCAN
rs213228	ZKSCAN3	cis	Thyroid	GTEx
rs213228	HIST1H2BL	cis	cerebellum	SCAN
rs213228	ZKSCAN3	cis	parietal	SCAN
rs213228	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28318400-28332000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:28318400-28350800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:28324200-28331600	Weak transcription	Thymus	Thymus
4	chr6:28324400-28331600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:28324400-28332600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:28324400-28333000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr6:28324400-28333000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr6:28324400-28333200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:28324400-28336000	Weak transcription	GM12878-XiMat	blood
10	chr6:28324400-28347600	Weak transcription	NHDF-Ad	bronchial
11	chr6:28324400-28347800	Weak transcription	Fetal Brain Male	brain
12	chr6:28324400-28348200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr6:28324400-28357200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr6:28324400-28357600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:28324600-28331600	Weak transcription	Fetal Kidney	kidney
16	chr6:28324600-28331800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr6:28324600-28332000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:28324600-28332600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr6:28324600-28332600	Weak transcription	Brain Angular Gyrus	brain
20	chr6:28324600-28332600	Weak transcription	HSMM	muscle
21	chr6:28324600-28332800	Weak transcription	Fetal Heart	heart
22	chr6:28324600-28349400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:28324600-28349600	Weak transcription	NHEK	skin
24	chr6:28324600-28358600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr6:28324800-28331800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:28324800-28332000	Weak transcription	Esophagus	oesophagus
27	chr6:28324800-28341600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr6:28325000-28331400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:28325000-28331800	Weak transcription	NHLF	lung
30	chr6:28325000-28332200	Weak transcription	HepG2	liver
31	chr6:28325000-28333200	Weak transcription	HMEC	breast
32	chr6:28325200-28331400	Weak transcription	Gastric	stomach
33	chr6:28325200-28331400	Weak transcription	Right Ventricle	heart
34	chr6:28325200-28331400	Weak transcription	A549	lung
35	chr6:28325200-28331600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:28325200-28333000	Weak transcription	Dnd41	blood
37	chr6:28325200-28333000	Weak transcription	NH-A	brain
38	chr6:28325400-28332800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr6:28325400-28350800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:28325600-28333200	Weak transcription	HUVEC	blood vessel
41	chr6:28326800-28332800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:28326800-28335400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:28326800-28336200	Strong transcription	Adipose Nuclei	Adipose
44	chr6:28327000-28334800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:28327000-28334800	Strong transcription	Placenta	Placenta
46	chr6:28327000-28336200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr6:28327000-28336200	Strong transcription	Fetal Stomach	stomach
48	chr6:28327000-28337600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:28327200-28334600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:28327200-28335400	Strong transcription	Fetal Muscle Trunk	muscle

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