Variant report

Variant	rs1990444
Chromosome Location	chr7:69226592-69226593
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	chr7:69221100..69223201-chr7:69225003..69226739,2	K562	blood:
2	chr7:69215801..69218748-chr7:69224882..69226979,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1003404	0.97[ASN][1000 genomes]
rs10260553	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487947	0.87[ASN][1000 genomes]
rs12670658	0.92[ASN][1000 genomes]
rs1548748	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17140890	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs210602	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210605	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215354	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2533436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2533437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851486	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851493	0.97[ASN][1000 genomes]
rs2851519	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2851520	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	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548556	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569334	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628885	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs633927	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953849	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs917617	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv831021	chr7:69122169-69364491	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1021538	chr7:69130236-69575753	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv538917	chr7:69130236-69575753	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv817276	chr7:69130237-69736834	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1018749	chr7:69149029-69995112	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv3394718	chr7:69194534-69238432	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1027399	chr7:69197011-69239721	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv538918	chr7:69197011-69239721	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1990444	ZNF92	cis	parietal	SCAN
rs1990444	STAG3L4	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69217400-69237400	Weak transcription	Fetal Muscle Leg	muscle
2	chr7:69219200-69233600	Weak transcription	Left Ventricle	heart
3	chr7:69219600-69229400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr7:69220000-69227400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr7:69221400-69228400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr7:69221800-69229600	Weak transcription	Fetal Brain Male	brain
7	chr7:69223200-69226800	Weak transcription	Brain Substantia Nigra	brain
8	chr7:69223200-69229800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:69223200-69234000	Weak transcription	Brain Hippocampus Middle	brain
10	chr7:69223400-69228400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr7:69223400-69228800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:69223400-69229000	Weak transcription	Ovary	ovary
13	chr7:69223400-69234000	Weak transcription	Brain Anterior Caudate	brain
14	chr7:69223600-69228800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr7:69223800-69233800	Weak transcription	Fetal Lung	lung
16	chr7:69224000-69226600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr7:69224000-69226600	Weak transcription	Adipose Nuclei	Adipose
18	chr7:69224200-69228600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr7:69224200-69229200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr7:69224200-69234400	Weak transcription	Fetal Brain Female	brain
21	chr7:69224400-69227600	Weak transcription	GM12878-XiMat	blood
22	chr7:69225200-69238800	Weak transcription	Primary B cells from cord blood	blood
23	chr7:69226000-69226600	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr7:69226000-69226800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:69226000-69226800	Enhancers	Fetal Stomach	stomach
26	chr7:69226000-69227000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:69226000-69227000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr7:69226000-69227200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr7:69226000-69227600	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr7:69226200-69226800	Enhancers	Brain Germinal Matrix	brain
31	chr7:69226400-69226600	Weak transcription	Brain Angular Gyrus	brain
32	chr7:69226400-69226800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr7:69226400-69226800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr7:69226400-69227200	Enhancers	Colon Smooth Muscle	Colon
35	chr7:69226400-69228200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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