Variant report

Variant	rs11960688
Chromosome Location	chr5:179740066-179740067
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179739596..179742574-chr5:180022400..180024079,2	MCF-7	breast:
2	chr5:179735551..179737821-chr5:179739675..179741218,2	MCF-7	breast:
3	chr5:179553164..179556296-chr5:179740039..179742529,3	MCF-7	breast:
4	chr5:179739299..179743379-chr5:179893176..179898905,6	MCF-7	breast:
5	chr5:179739339..179743235-chr5:179757984..179764634,9	MCF-7	breast:
6	chr5:179738783..179741691-chr5:179897243..179899588,2	MCF-7	breast:
7	chr5:179739780..179742416-chr5:179755432..179756942,2	MCF-7	breast:
8	chr5:179601654..179603372-chr5:179739320..179741770,2	MCF-7	breast:
9	chr5:179737116..179741285-chr5:179920642..179923208,4	MCF-7	breast:
10	chr5:179738876..179741151-chr6:26204782..26206564,2	MCF-7	breast:
11	chr5:179739190..179742513-chr5:179779970..179783347,3	MCF-7	breast:
12	chr5:179718624..179722005-chr5:179739945..179743525,7	MCF-7	breast:
13	chr5:179724591..179726786-chr5:179739258..179741473,3	MCF-7	breast:
14	chr5:179717535..179723990-chr5:179738269..179745292,15	MCF-7	breast:
15	chr5:179739354..179741668-chr5:179785404..179788387,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000248367	Chromatin interaction
ENSG00000131459	Chromatin interaction
ENSG00000050748	Chromatin interaction
ENSG00000113300	Chromatin interaction
ENSG00000198518	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11249699	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11249704	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739985	1.00[ASN][1000 genomes]
rs11746060	1.00[ASN][1000 genomes]
rs11960633	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3095943	1.00[ASN][1000 genomes]
rs34293630	1.00[ASN][1000 genomes]
rs4425468	1.00[ASN][1000 genomes]
rs4700733	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700734	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66942438	1.00[ASN][1000 genomes]
rs6893651	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893693	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73811354	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7720553	1.00[ASN][1000 genomes]
rs7735562	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
4	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
5	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
6	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
7	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
8	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

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179720600-179742800	Weak transcription	Right Ventricle	heart
2	chr5:179720600-179743200	Weak transcription	Fetal Lung	lung
3	chr5:179720600-179756800	Weak transcription	NHDF-Ad	bronchial
4	chr5:179720600-179758400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:179720800-179743600	Weak transcription	Right Atrium	heart
6	chr5:179720800-179747000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr5:179721000-179740800	Weak transcription	Esophagus	oesophagus
8	chr5:179721000-179741000	Weak transcription	Colon Smooth Muscle	Colon
9	chr5:179721000-179741200	Weak transcription	Fetal Brain Male	brain
10	chr5:179721000-179743000	Weak transcription	Spleen	Spleen
11	chr5:179721800-179740800	Weak transcription	Gastric	stomach
12	chr5:179723200-179740800	Weak transcription	Pancreas	Pancrea
13	chr5:179723400-179740600	Weak transcription	Fetal Intestine Small	intestine
14	chr5:179725200-179740800	Weak transcription	Hela-S3	cervix
15	chr5:179726800-179750600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:179727000-179755800	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr5:179727200-179757400	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr5:179727200-179757400	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr5:179727400-179757600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:179727600-179757600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr5:179728600-179761400	Weak transcription	Aorta	Aorta
22	chr5:179728800-179750800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:179729600-179743200	Weak transcription	HSMM	muscle
24	chr5:179730600-179740800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr5:179730800-179750800	Weak transcription	HSMMtube	muscle
26	chr5:179731000-179742800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:179731200-179740600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr5:179731600-179740800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:179731600-179755600	Weak transcription	Fetal Brain Female	brain
30	chr5:179731800-179741200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:179732000-179740600	Weak transcription	Brain Germinal Matrix	brain
32	chr5:179732200-179750800	Weak transcription	Brain Substantia Nigra	brain
33	chr5:179732800-179751200	Weak transcription	Adipose Nuclei	Adipose
34	chr5:179733000-179740600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr5:179733600-179741200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:179733600-179744800	Weak transcription	Brain Hippocampus Middle	brain
37	chr5:179736600-179740600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr5:179736800-179751800	Weak transcription	Left Ventricle	heart
39	chr5:179737400-179750000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:179737600-179746200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr5:179737600-179750800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:179738000-179740200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr5:179738000-179758000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr5:179738200-179746200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr5:179738200-179755600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:179738600-179745200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr5:179738800-179740200	Weak transcription	Placenta	Placenta
48	chr5:179738800-179740800	Weak transcription	Fetal Muscle Leg	muscle
49	chr5:179738800-179740800	Weak transcription	Ovary	ovary
50	chr5:179738800-179741000	Weak transcription	Osteobl	bone

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