Variant report

Variant	rs2533437
Chromosome Location	chr7:69118778-69118779
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:2515862..2518355-chr7:69118525..69120604,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157870	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1003404	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10260553	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487947	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[ASN][1000 genomes]
rs12670658	0.92[ASN][1000 genomes]
rs1548748	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17140890	0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1990444	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210602	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210605	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215354	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2533436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2851486	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851493	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2851519	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2851520	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34701787	0.87[ASN][1000 genomes]
rs41848	0.92[ASN][1000 genomes]
rs41854	0.92[ASN][1000 genomes]
rs41857	0.92[ASN][1000 genomes]
rs4717522	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548556	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569334	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628885	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs633927	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953849	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs917617	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023885	chr7:68894896-69158290	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv538915	chr7:68894896-69158290	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv916011	chr7:68942155-69330800	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv428169	chr7:69021482-69196743	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2533437	ZNF92	cis	parietal	SCAN
rs2533437	STAG3L4	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69106200-69119000	Weak transcription	Brain Substantia Nigra	brain
2	chr7:69106200-69121600	Weak transcription	Fetal Kidney	kidney
3	chr7:69109200-69119000	Weak transcription	Fetal Stomach	stomach
4	chr7:69109400-69119400	Weak transcription	Fetal Brain Female	brain
5	chr7:69109400-69121800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr7:69109800-69119200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr7:69110000-69119400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr7:69111000-69121800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:69113000-69118800	Weak transcription	Brain Hippocampus Middle	brain
10	chr7:69114400-69119200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr7:69114400-69119200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr7:69114400-69121800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr7:69114600-69119200	Weak transcription	Brain Angular Gyrus	brain
14	chr7:69114600-69119200	Weak transcription	Esophagus	oesophagus
15	chr7:69114600-69119200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr7:69114800-69121400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:69115800-69119200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr7:69116000-69118800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:69116000-69119200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr7:69116200-69119600	Weak transcription	Right Atrium	heart
21	chr7:69116400-69118800	Weak transcription	Ovary	ovary
22	chr7:69116600-69119600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr7:69116800-69122600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr7:69117200-69120000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr7:69117600-69119200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr7:69117600-69120200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr7:69117800-69119800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr7:69118000-69118800	Flanking Active TSS	GM12878-XiMat	blood
29	chr7:69118000-69119400	Enhancers	Lung	lung
30	chr7:69118000-69120800	Enhancers	Fetal Heart	heart
31	chr7:69118000-69123000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr7:69118000-69125200	Enhancers	Fetal Lung	lung
33	chr7:69118200-69119000	Weak transcription	Adipose Nuclei	Adipose
34	chr7:69118200-69119200	Weak transcription	Colon Smooth Muscle	Colon
35	chr7:69118200-69121800	Weak transcription	Fetal Intestine Small	intestine
36	chr7:69118200-69122800	Enhancers	Brain Germinal Matrix	brain
37	chr7:69118400-69119800	Enhancers	Primary hematopoietic stem cells	blood
38	chr7:69118400-69121000	Enhancers	Primary B cells from cord blood	blood
39	chr7:69118600-69118800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr7:69118600-69119000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
41	chr7:69118600-69119400	Enhancers	Psoas Muscle	Psoas
42	chr7:69118600-69120800	Enhancers	Fetal Thymus	thymus
43	chr7:69118600-69121200	Enhancers	Brain Anterior Caudate	brain
44	chr7:69118600-69121200	Enhancers	Left Ventricle	heart
45	chr7:69118600-69122600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr7:69118600-69122600	Enhancers	Fetal Muscle Leg	muscle

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