Variant report

Variant	rs13223792
Chromosome Location	chr7:99675659-99675660
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:99611430..99615857-chr7:99675156..99681193,15	K562	blood:
2	chr7:99668310..99676246-chr7:99677185..99681836,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106261	Chromatin interaction
ENSG00000166526	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10228764	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10267212	0.82[CEU][hapmap]
rs10281368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1060544	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1076237	0.81[CEU][hapmap]
rs11771139	0.83[CHB][hapmap];0.98[GIH][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap]
rs11771331	0.86[MEX][hapmap]
rs12705070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12705071	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs13232115	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1527423	0.82[YRI][hapmap]
rs1534310	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1880949	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap]
rs2070215	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs2293479	0.91[CEU][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34031156	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35146811	0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap]
rs4134903	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4424195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4729566	0.85[MEX][hapmap]
rs4729576	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59261051	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6465760	0.82[CEU][hapmap]
rs6465761	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6465762	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6950205	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6953441	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6974305	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7788746	0.86[MEX][hapmap]
rs999885	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
6	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs13223792	ZSCAN21	cis	parietal	SCAN
rs13223792	ZKSCAN1	cis	cerebellum	SCAN
rs13223792	SERPINE1	cis	cerebellum	SCAN
rs13223792	LRRC17	cis	parietal	SCAN
rs13223792	GAL3ST4	cis	cerebellum	SCAN
rs13223792	ZNF498	cis	cerebellum	SCAN
rs13223792	GATS	cis	parietal	SCAN
rs13223792	GATS	cis	cerebellum	SCAN
rs13223792	BUD31	cis	parietal	SCAN
rs13223792	PILRB	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99666400-99677200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:99666400-99678000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:99666800-99677000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:99669600-99677600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:99670200-99676600	Strong transcription	Stomach Smooth Muscle	stomach
6	chr7:99670400-99676200	Strong transcription	Brain Hippocampus Middle	brain
7	chr7:99670400-99676400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr7:99670400-99676600	Strong transcription	Placenta Amnion	Placenta Amnion
9	chr7:99670400-99677000	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr7:99670600-99676000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr7:99670600-99677400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:99670600-99677600	Strong transcription	Primary T cells from cord blood	blood
13	chr7:99670800-99675800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr7:99670800-99676400	Strong transcription	Dnd41	blood
15	chr7:99670800-99677000	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr7:99670800-99677400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr7:99670800-99677400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr7:99671000-99676400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:99671000-99676600	Weak transcription	Right Atrium	heart
20	chr7:99671000-99676800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:99671000-99676800	Strong transcription	Fetal Brain Female	brain
22	chr7:99671000-99676800	Weak transcription	Psoas Muscle	Psoas
23	chr7:99671000-99677000	Strong transcription	Placenta	Placenta
24	chr7:99671000-99677000	Strong transcription	NHEK	skin
25	chr7:99671000-99677200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr7:99671000-99677200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:99671000-99677400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:99671400-99676800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr7:99671400-99677400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr7:99671400-99677400	Strong transcription	HUVEC	blood vessel
31	chr7:99671600-99677400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr7:99671800-99677000	Strong transcription	Fetal Muscle Trunk	muscle
33	chr7:99671800-99677200	Strong transcription	NH-A	brain
34	chr7:99672000-99676600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr7:99672000-99676600	Strong transcription	Brain Germinal Matrix	brain
36	chr7:99672000-99677000	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr7:99672000-99677000	Strong transcription	Fetal Thymus	thymus
38	chr7:99672000-99677200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr7:99672400-99677000	Weak transcription	Small Intestine	intestine
40	chr7:99673000-99676400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr7:99673000-99676600	Strong transcription	Fetal Lung	lung
42	chr7:99673000-99677600	Strong transcription	Osteobl	bone
43	chr7:99673000-99677800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr7:99673200-99676800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr7:99673400-99676800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr7:99673400-99677400	Weak transcription	NHDF-Ad	bronchial
47	chr7:99673400-99677600	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr7:99673400-99677600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr7:99673400-99677800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr7:99673400-99677800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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