Variant report

Variant	rs4414938
Chromosome Location	chr4:8549206-8549207
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:8548072..8551323-chr4:8572516..8575493,5	MCF-7	breast:
2	chr4:8466177..8468891-chr4:8548337..8550041,2	MCF-7	breast:
3	chr4:8499473..8501004-chr4:8548114..8550892,2	K562	blood:
4	chr4:8538338..8543611-chr4:8548493..8553766,7	MCF-7	breast:
5	chr4:8542053..8545358-chr4:8547295..8551816,4	MCF-7	breast:
6	chr4:8460049..8461557-chr4:8548208..8550640,2	MCF-7	breast:
7	chr4:8547302..8552930-chr4:8559663..8563639,8	MCF-7	breast:
8	chr4:8501425..8503291-chr4:8548491..8551263,2	MCF-7	breast:
9	chr4:8548779..8551744-chr4:8562159..8565274,3	MCF-7	breast:
10	chr4:8535273..8538017-chr4:8547280..8549775,3	MCF-7	breast:
11	chr4:8548395..8550784-chr4:8562641..8564902,2	K562	blood:
12	chr4:8544480..8546948-chr4:8548054..8550987,2	K562	blood:
13	chr4:8470409..8471154-chr4:8548815..8549418,2	MCF-7	breast:
14	chr4:8490067..8491985-chr4:8548125..8550420,2	MCF-7	breast:
15	chr4:8525437..8527279-chr4:8549040..8551142,2	MCF-7	breast:
16	chr4:8547587..8550346-chr4:8589117..8591927,3	MCF-7	breast:
17	chr4:8548872..8549469-chr4:8586632..8587168,2	MCF-7	breast:
18	chr4:8470194..8471378-chr4:8548265..8549392,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000155269	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10805208	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10805209	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10938720	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10938721	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10938722	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10938723	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11723202	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11732364	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11736996	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17204393	0.83[EUR][1000 genomes]
rs3103086	0.89[ASN][1000 genomes]
rs3115408	0.84[ASN][1000 genomes]
rs34257763	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4449400	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4561917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4996699	0.84[ASN][1000 genomes]
rs55723892	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56379295	0.88[EUR][1000 genomes]
rs61570587	0.82[EUR][1000 genomes]
rs7668839	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7674109	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7687248	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[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	nsv461221	chr4:8534283-8554894	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv593640	chr4:8534283-8554894	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4414938	C4orf23	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8544400-8551600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:8544400-8552600	Enhancers	Placenta	Placenta
3	chr4:8544800-8549600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:8544800-8556600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:8546600-8550200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:8546800-8551000	Weak transcription	Spleen	Spleen
7	chr4:8547600-8549400	Weak transcription	NHLF	lung
8	chr4:8547600-8552400	Weak transcription	HSMMtube	muscle
9	chr4:8547800-8550200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:8548400-8550000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:8548800-8549400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:8548800-8549800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:8548800-8549800	Enhancers	Muscle Satellite Cultured Cells	--
14	chr4:8548800-8549800	Enhancers	Stomach Mucosa	stomach
15	chr4:8548800-8549800	Enhancers	NH-A	brain
16	chr4:8548800-8550000	Enhancers	NHDF-Ad	bronchial
17	chr4:8548800-8550000	Enhancers	Osteobl	bone
18	chr4:8548800-8550600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:8548800-8550800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:8548800-8551400	Enhancers	Placenta Amnion	Placenta Amnion
21	chr4:8549000-8549400	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr4:8549000-8549400	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr4:8549000-8549400	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr4:8549000-8549400	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr4:8549000-8549600	Enhancers	H1 Cell Line	embryonic stem cell
26	chr4:8549000-8549600	Flanking Active TSS	K562	blood
27	chr4:8549000-8549800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr4:8549000-8549800	Enhancers	HSMM	muscle
29	chr4:8549000-8550000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:8549000-8550000	Enhancers	NHEK	skin
31	chr4:8549000-8550200	Enhancers	HMEC	breast
32	chr4:8549000-8550800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:8549000-8551200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr4:8549200-8549400	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr4:8549200-8549600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr4:8549200-8549600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr4:8549200-8549800	Enhancers	A549	lung
38	chr4:8549200-8550000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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