Variant report

Variant	rs7533588
Chromosome Location	chr1:227942842-227942843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227941103..227943763-chr1:228134679..228136667,2	MCF-7	breast:
2	chr1:227936020..227939973-chr1:227940260..227944026,6	K562	blood:
3	chr1:227932429..227934376-chr1:227940770..227943766,2	K562	blood:

Variant related genes	Relation type
ENSG00000143816	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1056699	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1060295	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799430	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10799439	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10916171	0.88[CEU][hapmap];0.82[MEX][hapmap]
rs10916188	0.82[EUR][1000 genomes]
rs10916191	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10916203	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1111046	0.85[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1155807	0.92[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12025942	0.88[CEU][hapmap]
rs12033610	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs1810680	0.92[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs1923823	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2104245	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2236360	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2236361	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4500311	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4653856	0.92[CEU][hapmap];0.80[JPT][hapmap]
rs6426468	0.92[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6426473	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6660432	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6693054	0.92[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6703846	0.92[CEU][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs730684	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7522634	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7526184	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534403	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7536765	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7539282	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552193	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9786978	0.89[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9969994	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv468238	chr1:227935762-228045748	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv549272	chr1:227935762-228045748	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7533588	ZNF678	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227924200-227946800	Weak transcription	HUVEC	blood vessel
2	chr1:227924200-227955000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:227930200-227945600	Weak transcription	NH-A	brain
4	chr1:227932800-227947200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:227933000-227946400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:227934000-227948800	Strong transcription	Primary T cells from cord blood	blood
7	chr1:227934200-227945400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:227934400-227950000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:227934800-227943200	Strong transcription	Fetal Intestine Large	intestine
10	chr1:227934800-227950200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:227934800-227950400	Strong transcription	Fetal Intestine Small	intestine
12	chr1:227935000-227949600	Strong transcription	Dnd41	blood
13	chr1:227935200-227949800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:227936400-227944400	Weak transcription	Aorta	Aorta
15	chr1:227936400-227946200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:227936400-227946600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:227936600-227945000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:227936600-227945000	Weak transcription	Fetal Kidney	kidney
19	chr1:227937000-227943400	Weak transcription	Fetal Lung	lung
20	chr1:227937200-227949600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:227937400-227943800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:227937400-227944400	Strong transcription	Fetal Thymus	thymus
23	chr1:227937400-227946000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:227937600-227946000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:227938000-227945000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:227938000-227950200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:227938400-227946800	Weak transcription	HMEC	breast
28	chr1:227938600-227943600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:227938600-227944000	Weak transcription	NHEK	skin
30	chr1:227938600-227946800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr1:227938600-227950400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:227938800-227943400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:227939000-227945400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:227939200-227943400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:227939200-227943600	Weak transcription	Adipose Nuclei	Adipose
36	chr1:227939200-227943600	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr1:227939200-227946000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:227939200-227946600	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr1:227939200-227946800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr1:227939200-227947000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:227939400-227943400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:227939400-227943600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:227939400-227944400	Weak transcription	A549	lung
44	chr1:227939400-227944800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:227939400-227945000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:227939400-227945600	Weak transcription	Liver	Liver
47	chr1:227939400-227945800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:227939400-227946200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr1:227939400-227946800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr1:227939400-227946800	Enhancers	Skeletal Muscle Female	skeletal muscle

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