Variant report

Variant	rs56005965
Chromosome Location	chr5:179954394-179954395
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	chr5:179943961..179945573-chr5:179952586..179955313,2	MCF-7	breast:
2	chr5:179954302..179955834-chr5:179973302..179975583,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11249715	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11249724	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11738060	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11740121	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11740213	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11740953	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11741030	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11742350	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11742375	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11744382	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11744428	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11744582	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11745477	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11745688	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11746130	0.85[EUR][1000 genomes]
rs11748724	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11748792	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11750477	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11750835	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11949203	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11956078	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11957507	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11960298	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12109328	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12110046	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12719870	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13156947	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13171439	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13171609	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13171921	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13174480	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13179742	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13181735	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13182919	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13183429	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13187624	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17630549	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17698422	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35076338	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35197594	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35490561	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56039468	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60034484	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62405496	0.81[EUR][1000 genomes]
rs62405525	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62405531	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62405532	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62405547	0.86[AMR][1000 genomes];0.96[EUR][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	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	nsv1023537	chr5:179791679-179982822	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv537985	chr5:179791679-179982822	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv1019519	chr5:179866730-179959408	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	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
12	esv1810959	chr5:179945112-179997861	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179923600-179957000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr5:179924600-179957000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:179927000-179954400	Weak transcription	Hela-S3	cervix
4	chr5:179929000-179959200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:179933800-179959000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:179934200-179956600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:179936800-179956200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr5:179938800-179956600	Weak transcription	HSMM	muscle
9	chr5:179942000-179956400	Weak transcription	Brain Germinal Matrix	brain
10	chr5:179942000-179958800	Weak transcription	Esophagus	oesophagus
11	chr5:179942600-179959000	Weak transcription	HepG2	liver
12	chr5:179942800-179954600	Weak transcription	Fetal Intestine Large	intestine
13	chr5:179946000-179958400	Weak transcription	Lung	lung
14	chr5:179946200-179960800	Weak transcription	NHLF	lung
15	chr5:179946400-179956800	Weak transcription	Osteobl	bone
16	chr5:179946600-179956200	Weak transcription	NH-A	brain
17	chr5:179946800-179959000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:179947000-179958000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr5:179948400-179956600	Weak transcription	A549	lung
20	chr5:179949000-179954400	Weak transcription	Primary B cells from cord blood	blood
21	chr5:179949000-179956800	Weak transcription	HMEC	breast
22	chr5:179949600-179956400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:179949800-179958800	Weak transcription	Aorta	Aorta
24	chr5:179950000-179954600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:179950000-179954600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:179950000-179954600	Weak transcription	Pancreas	Pancrea
27	chr5:179950000-179956600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr5:179950200-179954600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr5:179950200-179954600	Weak transcription	Gastric	stomach
30	chr5:179950200-179955600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr5:179950200-179956600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr5:179950200-179956800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:179950200-179958600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:179950200-179959000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr5:179950200-179959200	Weak transcription	Brain Anterior Caudate	brain
36	chr5:179950200-179959200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr5:179950200-179959800	Weak transcription	Left Ventricle	heart
38	chr5:179950200-179975200	Weak transcription	Psoas Muscle	Psoas
39	chr5:179950200-179984400	Weak transcription	NHDF-Ad	bronchial
40	chr5:179950200-179992000	Weak transcription	Right Ventricle	heart
41	chr5:179950400-179992400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr5:179950600-179959400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr5:179950600-180004000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr5:179950800-179954600	Weak transcription	Fetal Stomach	stomach
45	chr5:179950800-179956200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr5:179950800-179956400	Weak transcription	Fetal Brain Female	brain
47	chr5:179950800-179956600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:179950800-179956600	Weak transcription	Brain Substantia Nigra	brain
49	chr5:179950800-179959000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr5:179951000-179956200	Weak transcription	Primary B cells from peripheral blood	blood

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