Variant report

Variant	rs4700931
Chromosome Location	chr5:179728707-179728708
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	chr5:179728336..179731115-chr5:179738243..179739763,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1035412	0.82[LWK][hapmap]
rs1363517	0.82[LWK][hapmap]
rs2386853	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3828688	0.96[ASN][1000 genomes]
rs4700932	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888925	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	esv2758032	chr5:179534477-179729944	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv2759398	chr5:179534477-179729944	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
8	nsv883290	chr5:179712060-179818868	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv830563	chr5:179717693-179898609	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv10787	chr5:179717724-179732388	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4700931	NOP16	cis	parietal	SCAN
rs4700931	OR2Y1	cis	cerebellum	SCAN
rs4700931	C5orf45	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179720600-179729600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:179720600-179730400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr5:179720600-179731400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr5:179720600-179739200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr5:179720600-179742800	Weak transcription	Right Ventricle	heart
6	chr5:179720600-179743200	Weak transcription	Fetal Lung	lung
7	chr5:179720600-179756800	Weak transcription	NHDF-Ad	bronchial
8	chr5:179720600-179758400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:179720800-179730200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:179720800-179743600	Weak transcription	Right Atrium	heart
11	chr5:179720800-179747000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr5:179721000-179729400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:179721000-179730200	Weak transcription	Brain Angular Gyrus	brain
14	chr5:179721000-179730400	Weak transcription	Adipose Nuclei	Adipose
15	chr5:179721000-179733600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:179721000-179740800	Weak transcription	Esophagus	oesophagus
17	chr5:179721000-179741000	Weak transcription	Colon Smooth Muscle	Colon
18	chr5:179721000-179741200	Weak transcription	Fetal Brain Male	brain
19	chr5:179721000-179743000	Weak transcription	Spleen	Spleen
20	chr5:179721200-179731400	Weak transcription	A549	lung
21	chr5:179721800-179740800	Weak transcription	Gastric	stomach
22	chr5:179723200-179740800	Weak transcription	Pancreas	Pancrea
23	chr5:179723400-179730400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr5:179723400-179731200	Weak transcription	Brain Germinal Matrix	brain
25	chr5:179723400-179740600	Weak transcription	Fetal Intestine Small	intestine
26	chr5:179723600-179729400	Weak transcription	HSMMtube	muscle
27	chr5:179725200-179740800	Weak transcription	Hela-S3	cervix
28	chr5:179726800-179734800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr5:179726800-179735000	Strong transcription	Osteobl	bone
30	chr5:179726800-179750600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:179727000-179728800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:179727000-179729000	Strong transcription	Fetal Muscle Trunk	muscle
33	chr5:179727000-179735000	Strong transcription	Fetal Stomach	stomach
34	chr5:179727000-179755800	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr5:179727200-179729000	Strong transcription	Placenta	Placenta
36	chr5:179727200-179729600	Strong transcription	HSMM	muscle
37	chr5:179727200-179734000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:179727200-179734800	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr5:179727200-179734800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:179727200-179757400	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr5:179727200-179757400	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr5:179727400-179728800	Strong transcription	Fetal Brain Female	brain
43	chr5:179727400-179730600	Enhancers	HepG2	liver
44	chr5:179727400-179731800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr5:179727400-179734400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr5:179727400-179734600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr5:179727400-179734600	Strong transcription	Ovary	ovary
48	chr5:179727400-179739800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr5:179727400-179740000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr5:179727400-179757600	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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