Variant report

Variant	rs3789823
Chromosome Location	chr7:150951819-150951820
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	chr7:150938571..150942838-chr7:150950941..150954111,4	MCF-7	breast:
2	chr7:150928662..150932139-chr7:150946772..150952684,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000033100	Chromatin interaction
ENSG00000082014	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12668799	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs219229	0.90[CHB][hapmap];0.84[CHD][hapmap];0.86[LWK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs219230	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs219233	0.90[CHB][hapmap];0.84[CHD][hapmap];0.86[LWK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs2252694	0.84[AFR][1000 genomes]
rs2487157	0.81[CHB][hapmap];0.84[CHD][hapmap];0.90[YRI][hapmap]
rs2530458	1.00[ASN][1000 genomes]
rs2530459	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2608289	0.81[CHB][hapmap];0.84[CHD][hapmap];0.90[YRI][hapmap]
rs2608290	0.81[CHB][hapmap];0.95[YRI][hapmap]
rs3807387	0.90[CHB][hapmap];0.84[CHD][hapmap];0.83[LWK][hapmap];0.95[YRI][hapmap]
rs4236429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4236430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4472433	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58125572	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7786030	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821419	chr7:150593315-150974269	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
2	nsv889476	chr7:150729212-150951819	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	120 gene(s)	inside rSNPs	diseases
3	nsv609035	chr7:150896223-150955765	Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv889487	chr7:150922952-150988172	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
5	nsv889488	chr7:150926775-150955765	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
6	nsv465216	chr7:150951819-150991795	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	nsv609036	chr7:150951819-150991795	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3789823	ABCF2	Cis_1M	lymphoblastoid	RTeQTL
rs3789823	ZNF212	cis	cerebellum	SCAN
rs3789823	ABCF2	cis	Thyroid	GTEx
rs3789823	GIMAP8	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150950000-150952000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:150950000-150952800	Enhancers	Right Ventricle	heart
3	chr7:150950200-150952800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
4	chr7:150950200-150953600	Weak transcription	Brain Anterior Caudate	brain
5	chr7:150950200-150953600	Weak transcription	Brain Hippocampus Middle	brain
6	chr7:150950400-150952000	Weak transcription	Ovary	ovary
7	chr7:150950400-150952200	Enhancers	Fetal Brain Male	brain
8	chr7:150950400-150973400	Weak transcription	Brain Substantia Nigra	brain
9	chr7:150950600-150952400	Enhancers	Fetal Muscle Leg	muscle
10	chr7:150950600-150952600	Weak transcription	Colon Smooth Muscle	Colon
11	chr7:150950600-150953600	Weak transcription	Gastric	stomach
12	chr7:150950600-150953800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr7:150950600-150955400	Weak transcription	Lung	lung
14	chr7:150950600-150955600	Weak transcription	Esophagus	oesophagus
15	chr7:150950600-150957200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr7:150950600-150957800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr7:150950600-150958400	Weak transcription	Right Atrium	heart
18	chr7:150950600-150961400	Weak transcription	Spleen	Spleen
19	chr7:150950600-150965200	Weak transcription	Brain Angular Gyrus	brain
20	chr7:150950600-150967600	Weak transcription	Pancreas	Pancrea
21	chr7:150950800-150953600	Weak transcription	Fetal Heart	heart
22	chr7:150951000-150965400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr7:150951000-150969800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr7:150951000-150970800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr7:150951200-150952000	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr7:150951200-150952600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:150951200-150952800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr7:150951200-150953600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr7:150951600-150952600	Enhancers	Stomach Smooth Muscle	stomach
30	chr7:150951600-150968000	Weak transcription	Brain Germinal Matrix	brain
31	chr7:150951800-150952600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr7:150951800-150953600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr7:150951800-150967600	Weak transcription	Fetal Brain Female	brain

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