Variant report

Variant	rs2416189
Chromosome Location	chr5:107712059-107712060
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	chr5:107705977..107708184-chr5:107711910..107713807,2	MCF-7	breast:
2	chr5:107704058..107705992-chr5:107711279..107713882,3	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10477892	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10477895	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13153782	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13161833	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13162979	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13173916	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13190222	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1355375	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1544741	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs158606	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs158607	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1588496	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17161232	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17385448	0.84[EUR][1000 genomes]
rs17452232	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1828457	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1849012	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1862196	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2052464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2416190	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2900034	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2900122	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2941693	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2941694	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2941697	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2966824	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2966830	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2966832	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2966834	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34261817	0.85[EUR][1000 genomes]
rs34409	0.81[EUR][1000 genomes]
rs34413	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34414	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34527417	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34747859	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34771507	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34854088	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35903369	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4438862	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4957755	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62359544	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6594299	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6594300	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6896653	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71592749	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7711964	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7721104	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7724056	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9326726	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs988436	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs988437	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882683	chr5:107476501-107769095	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv882686	chr5:107564746-107769095	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv882688	chr5:107595383-107715746	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	esv2755544	chr5:107614101-107748101	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107697200-107715200	Weak transcription	HSMM	muscle
2	chr5:107698200-107715600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:107699000-107712800	Weak transcription	Right Ventricle	heart
4	chr5:107706400-107714200	Weak transcription	Left Ventricle	heart
5	chr5:107708600-107716200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:107709200-107712200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:107709600-107713800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:107709600-107714200	Weak transcription	Gastric	stomach
9	chr5:107709600-107715600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:107709600-107715600	Weak transcription	Thymus	Thymus
11	chr5:107709600-107716000	Weak transcription	Ovary	ovary
12	chr5:107709800-107715200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:107710000-107715600	Weak transcription	HSMMtube	muscle
14	chr5:107710200-107714400	Weak transcription	Primary T cells from cord blood	blood
15	chr5:107711000-107715600	Weak transcription	Fetal Thymus	thymus
16	chr5:107711400-107714200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr5:107711400-107715600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr5:107711600-107714200	Weak transcription	Psoas Muscle	Psoas
19	chr5:107711600-107715200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr5:107711800-107712800	Weak transcription	Fetal Heart	heart
21	chr5:107711800-107714200	Weak transcription	Small Intestine	intestine
22	chr5:107711800-107714800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr5:107712000-107714600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:107712000-107715000	Weak transcription	Fetal Lung	lung
25	chr5:107712000-107715400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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