Variant report

Variant	rs1551637
Chromosome Location	chr4:56051428-56051429
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:56050488..56051475-chr4:56187155..56188482,6	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10012700	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10016792	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10019018	0.93[EUR][1000 genomes]
rs10030224	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10213072	0.84[EUR][1000 genomes]
rs11133363	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11133364	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11133365	0.90[EUR][1000 genomes]
rs12152606	0.84[EUR][1000 genomes]
rs12504287	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12509589	0.90[EUR][1000 genomes]
rs12645088	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12716020	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12716021	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13107781	0.90[EUR][1000 genomes]
rs13115127	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13139198	0.89[EUR][1000 genomes]
rs13143119	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13143543	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1380072	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1380073	0.84[EUR][1000 genomes]
rs1551636	0.90[EUR][1000 genomes]
rs1551638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17081850	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17081852	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17081854	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17081857	0.84[EUR][1000 genomes]
rs1870376	0.80[EUR][1000 genomes]
rs1870381	0.90[EUR][1000 genomes]
rs1870382	0.90[EUR][1000 genomes]
rs1993583	0.80[EUR][1000 genomes]
rs1993584	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1993585	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1993586	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2015048	0.84[EUR][1000 genomes]
rs2085620	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2085621	0.84[EUR][1000 genomes]
rs2125486	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2125487	0.80[EUR][1000 genomes]
rs2125488	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2899030	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3986296	0.80[EUR][1000 genomes]
rs4241993	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4277836	0.84[EUR][1000 genomes]
rs4304028	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4458511	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4864960	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4864961	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6554240	0.80[EUR][1000 genomes]
rs6554241	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6554242	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6810735	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6812621	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6852640	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6853855	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs733378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7435539	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7696873	0.84[EUR][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	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1551637	NMU	cis	cerebellum	SCAN
rs1551637	SPINK2	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56046800-56054200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr4:56047800-56053800	Enhancers	HUVEC	blood vessel
3	chr4:56048800-56052000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr4:56048800-56052400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:56049000-56052400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:56049200-56052000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:56049200-56052200	Enhancers	HMEC	breast
8	chr4:56049200-56054200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr4:56049600-56051600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:56049600-56051800	Enhancers	Osteobl	bone
11	chr4:56049600-56052000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:56049800-56051600	Enhancers	Placenta Amnion	Placenta Amnion
13	chr4:56049800-56051800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:56049800-56052000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:56050000-56051800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:56050200-56052800	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr4:56050200-56054000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr4:56050200-56054200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr4:56050200-56054600	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr4:56050200-56054600	Enhancers	H9 Cell Line	embryonic stem cell
21	chr4:56050400-56051600	Enhancers	HSMMtube	muscle
22	chr4:56050400-56052600	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr4:56050600-56051600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr4:56050600-56051600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:56050600-56051600	Enhancers	Right Atrium	heart
26	chr4:56050600-56052000	Enhancers	Ovary	ovary
27	chr4:56050600-56052200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:56050600-56053400	Enhancers	Fetal Lung	lung
29	chr4:56051000-56051600	Enhancers	NH-A	brain
30	chr4:56051000-56051800	Enhancers	Muscle Satellite Cultured Cells	--
31	chr4:56051000-56052000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr4:56051000-56052000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr4:56051000-56052200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:56051000-56053400	Enhancers	Fetal Heart	heart
35	chr4:56051000-56054400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:56051000-56054600	Weak transcription	Lung	lung
37	chr4:56051200-56052200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:56051200-56052200	Enhancers	Fetal Muscle Leg	muscle
39	chr4:56051200-56052200	Enhancers	NHLF	lung
40	chr4:56051200-56052400	Enhancers	Fetal Stomach	stomach
41	chr4:56051200-56054800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:56051400-56051800	Enhancers	NHEK	skin
43	chr4:56051400-56052200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr4:56051400-56052200	Enhancers	NHDF-Ad	bronchial
45	chr4:56051400-56054400	Weak transcription	Left Ventricle	heart

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