Variant report

Variant	rs3103074
Chromosome Location	chr4:8562668-8562669
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:8548779..8551744-chr4:8562159..8565274,3	MCF-7	breast:
2	chr4:8561336..8563583-chr4:8582285..8585156,2	MCF-7	breast:
3	chr4:8472633..8474433-chr4:8561058..8562911,2	K562	blood:
4	chr4:8562627..8565501-chr4:8586940..8588652,2	MCF-7	breast:
5	chr4:8548395..8550784-chr4:8562641..8564902,2	K562	blood:

Variant related genes	Relation type
ENSG00000155275	Chromatin interaction
ENSG00000155269	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11944845	1.00[JPT][hapmap]
rs13116227	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13132489	0.82[ASN][1000 genomes]
rs17204647	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2004768	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3115384	0.82[ASN][1000 genomes]
rs3115390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv878612	chr4:8534283-8618916	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv1832730	chr4:8541086-9514568	Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
5	esv1843578	chr4:8541086-9514568	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
6	nsv878613	chr4:8554894-8618916	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv878614	chr4:8554894-8669619	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3103074	BMP7	trans	parietal	SCAN
rs3103074	STK32B	cis	cerebellum	SCAN
rs3103074	HTRA3	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8549400-8568400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr4:8556800-8562800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:8560800-8562800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr4:8560800-8564200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:8561200-8564000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:8561800-8562800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr4:8561800-8563000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:8561800-8563000	Flanking Active TSS	Placenta	Placenta
9	chr4:8561800-8563000	Enhancers	Osteobl	bone
10	chr4:8562000-8562800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr4:8562000-8563000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr4:8562000-8563000	Enhancers	H1 Cell Line	embryonic stem cell
13	chr4:8562000-8563000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:8562000-8563000	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr4:8562000-8563000	Enhancers	NHDF-Ad	bronchial
16	chr4:8562200-8562800	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr4:8562200-8562800	Enhancers	A549	lung
18	chr4:8562200-8563000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:8562200-8563000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:8562400-8563000	Enhancers	GM12878-XiMat	blood
21	chr4:8562400-8563000	Enhancers	HSMM	muscle
22	chr4:8562400-8563400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:8562400-8564000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:8562600-8562800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:8562600-8562800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:8562600-8562800	Enhancers	HSMMtube	muscle
27	chr4:8562600-8562800	Enhancers	NH-A	brain
28	chr4:8562600-8563000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:8562600-8563000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:8562600-8563000	Enhancers	Fetal Lung	lung
31	chr4:8562600-8563600	Weak transcription	Placenta Amnion	Placenta Amnion

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