Variant report

Variant	rs12521640
Chromosome Location	chr5:179756818-179756819
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179739780..179742416-chr5:179755432..179756942,2	MCF-7	breast:
2	chr5:179755365..179757615-chr5:179761406..179763311,3	K562	blood:
3	chr5:179719106..179721039-chr5:179754091..179757820,3	MCF-7	breast:
4	chr5:179753387..179757614-chr5:179776973..179781058,5	MCF-7	breast:
5	chr5:179723581..179725108-chr5:179754464..179757151,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131459	Chromatin interaction
ENSG00000248367	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs3749788	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
9	nsv1031836	chr5:179742033-180676122	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
10	nsv537984	chr5:179742033-180676122	Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
11	nsv949199	chr5:179743553-180696889	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
12	nsv883291	chr5:179755559-179818868	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179720600-179758400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:179727200-179757400	Strong transcription	H1 Cell Line	embryonic stem cell
3	chr5:179727200-179757400	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:179727400-179757600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:179727600-179757600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:179728600-179761400	Weak transcription	Aorta	Aorta
7	chr5:179738000-179758000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:179739600-179761200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr5:179740400-179757400	Weak transcription	NHLF	lung
10	chr5:179740600-179757600	Strong transcription	H9 Cell Line	embryonic stem cell
11	chr5:179741600-179757600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr5:179741600-179762600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr5:179741800-179758200	Weak transcription	Fetal Intestine Small	intestine
14	chr5:179742000-179757400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr5:179742600-179757800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
16	chr5:179743200-179761000	Weak transcription	Right Ventricle	heart
17	chr5:179743400-179758200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr5:179743800-179757400	Weak transcription	Fetal Lung	lung
19	chr5:179744000-179766600	Weak transcription	Gastric	stomach
20	chr5:179746000-179760800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:179746000-179761400	Weak transcription	Right Atrium	heart
22	chr5:179749200-179757400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:179750200-179757400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr5:179751800-179757400	Weak transcription	HSMMtube	muscle
25	chr5:179752200-179759000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr5:179752400-179757400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:179752400-179758800	Weak transcription	Left Ventricle	heart
28	chr5:179752400-179760800	Weak transcription	Brain Germinal Matrix	brain
29	chr5:179752400-179760800	Weak transcription	Brain Substantia Nigra	brain
30	chr5:179752600-179758800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr5:179754000-179758200	Strong transcription	Fetal Stomach	stomach
32	chr5:179754000-179758800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr5:179754200-179758800	Strong transcription	Fetal Muscle Trunk	muscle
34	chr5:179754400-179758200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:179754400-179758800	Strong transcription	Fetal Muscle Leg	muscle
36	chr5:179754600-179757000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:179754600-179757200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr5:179754600-179758200	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr5:179754800-179757000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr5:179754800-179757400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:179754800-179758200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:179755000-179759800	Enhancers	Placenta	Placenta
43	chr5:179755200-179758800	Strong transcription	Brain Anterior Caudate	brain
44	chr5:179755600-179757200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:179755600-179757200	Strong transcription	Fetal Brain Female	brain
46	chr5:179755600-179757600	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr5:179755600-179757800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:179755800-179757400	Genic enhancers	A549	lung
49	chr5:179755800-179757600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr5:179755800-179758600	Weak transcription	Pancreas	Pancrea

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