Variant report

Variant	rs13171439
Chromosome Location	chr5:180008456-180008457
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:180004083..180005642-chr5:180006961..180009387,2	MCF-7	breast:
2	chr5:180007211..180008779-chr5:180011095..180013327,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNOT6-6	chr5:180007444-180008867	NONHSAT105687

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11249715	0.80[EUR][1000 genomes]
rs11249724	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11738060	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11740121	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11740213	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11740953	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11741030	0.81[EUR][1000 genomes]
rs11742350	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11742375	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11744382	0.80[EUR][1000 genomes]
rs11744428	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11744582	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11745477	0.80[EUR][1000 genomes]
rs11745688	0.81[EUR][1000 genomes]
rs11748724	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11748792	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11949203	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11956078	0.81[EUR][1000 genomes]
rs11957507	0.80[EUR][1000 genomes]
rs11960298	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12109328	0.81[EUR][1000 genomes]
rs12110046	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13156947	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13171609	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13171921	0.81[EUR][1000 genomes]
rs13174480	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13179742	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13181735	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13182919	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13183429	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13187624	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17630549	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17698422	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35076338	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35197594	0.81[EUR][1000 genomes]
rs56005965	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56039468	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60034484	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62405525	0.82[EUR][1000 genomes]
rs62405531	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62405532	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62405547	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv830564	chr5:179867394-180010096	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	esv2762572	chr5:179996987-180183359	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv533204	chr5:180008319-180273638	Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179994200-180013800	Weak transcription	NHEK	skin
2	chr5:179995200-180009200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr5:180001200-180008600	Weak transcription	Right Ventricle	heart
4	chr5:180001200-180012400	Weak transcription	Fetal Intestine Small	intestine
5	chr5:180001200-180012400	Weak transcription	Lung	lung
6	chr5:180001400-180008600	Weak transcription	Thymus	Thymus
7	chr5:180001400-180009600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:180001400-180010000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:180001400-180010400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr5:180001600-180010800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr5:180002600-180009200	Weak transcription	Fetal Brain Female	brain
12	chr5:180003400-180008800	Weak transcription	Fetal Stomach	stomach
13	chr5:180003600-180015600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:180003800-180009800	Weak transcription	HUVEC	blood vessel
15	chr5:180003800-180010000	Weak transcription	Osteobl	bone
16	chr5:180003800-180012200	Weak transcription	Primary T cells from cord blood	blood
17	chr5:180003800-180015000	Weak transcription	K562	blood
18	chr5:180004000-180008800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr5:180004600-180009200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr5:180004800-180011000	Weak transcription	NH-A	brain
21	chr5:180005000-180009800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:180005200-180008800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:180005600-180009200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr5:180005600-180011000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr5:180005600-180015000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:180005800-180008600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr5:180005800-180008600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:180005800-180008600	Weak transcription	A549	lung
29	chr5:180005800-180008800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr5:180005800-180009000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr5:180005800-180009000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr5:180005800-180009200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr5:180005800-180009200	Weak transcription	Fetal Intestine Large	intestine
34	chr5:180005800-180009400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:180005800-180009400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr5:180005800-180009400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr5:180005800-180009600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:180005800-180010400	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr5:180005800-180010600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:180005800-180010800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:180005800-180010800	Weak transcription	Fetal Heart	heart
42	chr5:180005800-180011000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr5:180005800-180013000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:180006000-180009400	Weak transcription	HSMM	muscle
45	chr5:180006000-180010600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr5:180006000-180011000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr5:180006400-180008600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr5:180006400-180010400	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr5:180006600-180009400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:180007000-180010800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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