Variant report

Variant	rs232878
Chromosome Location	chr1:59114128-59114129
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59037535..59044875-chr1:59111123..59123546,29	MCF-7	breast:
2	chr1:59010701..59012328-chr1:59112006..59114513,3	MCF-7	breast:
3	chr1:59112857..59115796-chr1:59116639..59119462,3	MCF-7	breast:
4	chr1:59036598..59046417-chr1:59110760..59123309,33	MCF-7	breast:
5	chr1:59112305..59114468-chr1:59114733..59116288,2	MCF-7	breast:
6	chr1:59046705..59048378-chr1:59112246..59114318,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184292	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11207300	0.81[EUR][1000 genomes]
rs15307	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs170828	0.93[EUR][1000 genomes]
rs232778	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs232779	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs232783	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs232788	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs232790	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs232857	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs232862	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs232863	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs232867	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs232877	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs232879	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs232880	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs232886	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs232901	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs232902	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs232904	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs232905	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs232906	0.91[EUR][1000 genomes]
rs232907	0.90[EUR][1000 genomes]
rs232908	0.90[EUR][1000 genomes]
rs232909	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs232910	0.90[EUR][1000 genomes]
rs232911	0.90[EUR][1000 genomes]
rs2746077	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2746083	0.83[EUR][1000 genomes]
rs4912369	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4912372	0.86[EUR][1000 genomes]
rs513436	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs542750	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6661922	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs675871	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs688225	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003930	chr1:58930444-59157038	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59093200-59115400	Weak transcription	NHEK	skin
2	chr1:59096000-59121600	Weak transcription	HUVEC	blood vessel
3	chr1:59096600-59121600	Weak transcription	Gastric	stomach
4	chr1:59102000-59130400	Weak transcription	Aorta	Aorta
5	chr1:59103600-59115200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:59104600-59115600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:59104600-59115600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:59108000-59115600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:59108200-59130400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:59108400-59115600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:59108600-59121600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:59108800-59114400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr1:59109000-59121600	Weak transcription	HepG2	liver
14	chr1:59109400-59121600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:59109600-59117800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:59109800-59115400	Weak transcription	Primary B cells from cord blood	blood
17	chr1:59109800-59115800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:59110400-59121600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr1:59110400-59123600	Weak transcription	HSMMtube	muscle
20	chr1:59110600-59114400	Weak transcription	Primary T cells from cord blood	blood
21	chr1:59110600-59119200	Weak transcription	Placenta	Placenta
22	chr1:59110800-59115400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:59110800-59125200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:59111600-59118200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:59112400-59121600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:59112600-59116200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:59112800-59115400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:59112800-59125600	Weak transcription	NHLF	lung

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