Variant report

Variant	rs11249704
Chromosome Location	chr5:179746391-179746392
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179744163..179746642-chr5:179892937..179895669,2	MCF-7	breast:
2	chr5:179744373..179746691-chr5:179749778..179751950,2	K562	blood:
3	chr5:179745198..179748984-chr5:179749617..179752058,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131459	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11249699	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739985	1.00[ASN][1000 genomes]
rs11746060	1.00[ASN][1000 genomes]
rs11960633	0.88[AMR][1000 genomes]
rs11960688	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095943	1.00[ASN][1000 genomes]
rs34293630	1.00[ASN][1000 genomes]
rs4425468	1.00[ASN][1000 genomes]
rs4700733	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700734	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66942438	1.00[ASN][1000 genomes]
rs6893651	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893693	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73811354	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7720553	1.00[ASN][1000 genomes]
rs7735562	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179720600-179756800	Weak transcription	NHDF-Ad	bronchial
2	chr5:179720600-179758400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:179720800-179747000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:179726800-179750600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:179727000-179755800	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr5:179727200-179757400	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr5:179727200-179757400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr5:179727400-179757600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:179727600-179757600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:179728600-179761400	Weak transcription	Aorta	Aorta
11	chr5:179728800-179750800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:179730800-179750800	Weak transcription	HSMMtube	muscle
13	chr5:179731600-179755600	Weak transcription	Fetal Brain Female	brain
14	chr5:179732200-179750800	Weak transcription	Brain Substantia Nigra	brain
15	chr5:179732800-179751200	Weak transcription	Adipose Nuclei	Adipose
16	chr5:179736800-179751800	Weak transcription	Left Ventricle	heart
17	chr5:179737400-179750000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr5:179737600-179750800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:179738000-179758000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:179738200-179755600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:179738800-179748600	Weak transcription	Lung	lung
22	chr5:179739600-179761200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr5:179740400-179757400	Weak transcription	NHLF	lung
24	chr5:179740600-179757600	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr5:179741000-179750600	Strong transcription	Osteobl	bone
26	chr5:179741200-179750400	Weak transcription	Esophagus	oesophagus
27	chr5:179741200-179754000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:179741400-179746800	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr5:179741400-179746800	Strong transcription	Fetal Stomach	stomach
30	chr5:179741400-179751000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:179741600-179750400	Weak transcription	Brain Germinal Matrix	brain
32	chr5:179741600-179756000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr5:179741600-179757600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr5:179741600-179762600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr5:179741800-179748600	Weak transcription	Colon Smooth Muscle	Colon
36	chr5:179741800-179758200	Weak transcription	Fetal Intestine Small	intestine
37	chr5:179742000-179757400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr5:179742600-179757800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
39	chr5:179743200-179761000	Weak transcription	Right Ventricle	heart
40	chr5:179743400-179750400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:179743400-179754200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:179743400-179758200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr5:179743800-179756400	Weak transcription	Colonic Mucosa	Colon
44	chr5:179743800-179757400	Weak transcription	Fetal Lung	lung
45	chr5:179744000-179766600	Weak transcription	Gastric	stomach
46	chr5:179744800-179746800	Strong transcription	A549	lung
47	chr5:179745000-179746400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr5:179745200-179747000	Strong transcription	NH-A	brain
49	chr5:179745400-179747000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
50	chr5:179745600-179747000	Strong transcription	HSMM	muscle

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