Variant report

Variant	rs880477
Chromosome Location	chr3:51377651-51377652
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:51376546..51378472-chr3:51379958..51381603,2	MCF-7	breast:
2	chr3:51373593..51375810-chr3:51376800..51379121,2	K562	blood:
3	chr3:51373184..51375093-chr3:51377621..51380061,2	K562	blood:
4	chr3:51367010..51371078-chr3:51375773..51379297,4	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12487468	1.00[YRI][hapmap]
rs12492615	1.00[YRI][hapmap]
rs12495561	0.90[YRI][hapmap]
rs1480366	0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17051685	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17051802	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2170177	0.91[YRI][hapmap]
rs4130473	1.00[YRI][hapmap]
rs4280628	1.00[AMR][1000 genomes]
rs4346580	0.91[YRI][hapmap]
rs4974112	0.91[YRI][hapmap]
rs57019473	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58075772	1.00[AMR][1000 genomes]
rs58807639	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59307262	1.00[AMR][1000 genomes]
rs61452834	1.00[AMR][1000 genomes]
rs61578076	1.00[AMR][1000 genomes]
rs72943888	1.00[AMR][1000 genomes]
rs72945711	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72945738	1.00[AMR][1000 genomes]
rs72945741	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951454	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951466	1.00[AMR][1000 genomes]
rs72951469	1.00[AMR][1000 genomes]
rs72951474	1.00[AMR][1000 genomes]
rs72951478	1.00[AMR][1000 genomes]
rs72951489	1.00[AMR][1000 genomes]
rs72953404	1.00[AMR][1000 genomes]
rs753452	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv20206	chr3:51344873-51415825	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs880477	HEMK	cis	multi-tissue	Pritchard

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51367600-51377800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:51369600-51383800	Weak transcription	Fetal Brain Male	brain
3	chr3:51372200-51377800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:51375000-51377800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:51375200-51377800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:51375400-51378000	Strong transcription	Fetal Brain Female	brain
7	chr3:51375600-51379000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:51376600-51377800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:51376600-51378800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:51376600-51379400	Enhancers	NHLF	lung
11	chr3:51376800-51377800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:51376800-51378400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:51376800-51378800	Enhancers	Aorta	Aorta
14	chr3:51376800-51379200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:51376800-51391800	Weak transcription	Brain Germinal Matrix	brain
16	chr3:51376800-51392400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:51377000-51378000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:51377000-51378600	Enhancers	Adipose Nuclei	Adipose
19	chr3:51377000-51378600	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr3:51377000-51379400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:51377200-51377800	Enhancers	HUVEC	blood vessel
22	chr3:51377200-51378000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:51377200-51378000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:51377200-51378200	Weak transcription	Placenta	Placenta
25	chr3:51377200-51378600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:51377200-51378600	Genic enhancers	Brain Hippocampus Middle	brain
27	chr3:51377200-51378800	Flanking Active TSS	A549	lung
28	chr3:51377400-51377800	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr3:51377400-51378000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:51377400-51378000	Flanking Active TSS	HSMM	muscle
31	chr3:51377400-51378000	Flanking Active TSS	HSMMtube	muscle
32	chr3:51377400-51378600	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr3:51377400-51378600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:51377400-51378600	Enhancers	Ovary	ovary
35	chr3:51377400-51378800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:51377400-51378800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr3:51377400-51378800	Enhancers	Stomach Mucosa	stomach
38	chr3:51377400-51379000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:51377400-51379000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:51377400-51379000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:51377400-51379200	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr3:51377400-51379400	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr3:51377400-51380000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:51377600-51377800	Enhancers	NHDF-Ad	bronchial
45	chr3:51377600-51378000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
46	chr3:51377600-51378000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:51377600-51378000	Flanking Active TSS	HMEC	breast
48	chr3:51377600-51378000	Flanking Active TSS	NH-A	brain
49	chr3:51377600-51378000	Flanking Active TSS	NHEK	skin
50	chr3:51377600-51378200	Enhancers	HUES48 Cell Line	embryonic stem cell

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