Variant report

Variant	rs1405688
Chromosome Location	chr4:102074134-102074135
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	chr4:102072492..102076401-chr4:102080849..102083286,3	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10516474	1.00[ASW][hapmap]
rs13102391	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13120190	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17829777	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17829885	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2732504	1.00[LWK][hapmap]
rs35057231	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35170337	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36096364	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71614680	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs71614681	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs71614682	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs71614683	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71614684	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1405688	MTMR4	trans	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102059400-102076600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:102062600-102090400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr4:102064200-102075200	Weak transcription	Primary B cells from cord blood	blood
4	chr4:102065400-102076200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:102065600-102076200	Weak transcription	HMEC	breast
6	chr4:102065800-102076200	Weak transcription	NHEK	skin
7	chr4:102068800-102077400	Weak transcription	Small Intestine	intestine
8	chr4:102069000-102078600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr4:102069200-102075000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:102069400-102074800	Weak transcription	Primary T cells from cord blood	blood
11	chr4:102070000-102075600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:102070000-102077000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr4:102070000-102078400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:102070600-102078200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:102070800-102074200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr4:102070800-102074200	Weak transcription	A549	lung
17	chr4:102071800-102074200	Weak transcription	Brain Angular Gyrus	brain
18	chr4:102071800-102074200	Weak transcription	Brain Anterior Caudate	brain
19	chr4:102071800-102074200	Weak transcription	Brain Hippocampus Middle	brain
20	chr4:102072000-102074200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr4:102072200-102076400	Weak transcription	Brain Substantia Nigra	brain
22	chr4:102072400-102077400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:102072800-102074200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr4:102073200-102076400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:102074000-102074600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:102074000-102075000	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr4:102074000-102075000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:102074000-102075200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:102074000-102075600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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