Variant report

Variant	rs1480366
Chromosome Location	chr3:51393374-51393375
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	chr3:51392857..51395304-chr3:51397366..51400297,3	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12487468	0.94[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes]
rs12492615	1.00[ASW][hapmap];0.94[LWK][hapmap];0.81[MKK][hapmap];0.91[YRI][hapmap]
rs12493323	0.81[AFR][1000 genomes]
rs12493978	0.82[MKK][hapmap]
rs12495561	0.81[YRI][hapmap]
rs17051685	1.00[ASW][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17051799	1.00[ASW][hapmap]
rs17051802	1.00[ASW][hapmap];0.88[LWK][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2170177	1.00[ASW][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.83[YRI][hapmap]
rs4130473	0.91[YRI][hapmap]
rs4280628	1.00[AMR][1000 genomes]
rs4346580	1.00[ASW][hapmap];0.94[LWK][hapmap];0.83[YRI][hapmap]
rs4468966	0.82[MKK][hapmap]
rs4974112	1.00[ASW][hapmap];0.94[LWK][hapmap];0.88[MKK][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs57019473	1.00[AMR][1000 genomes]
rs58075772	1.00[AMR][1000 genomes]
rs58807639	0.96[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	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72945738	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72945741	1.00[AMR][1000 genomes]
rs72951454	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]
rs751076	0.82[MKK][hapmap]
rs753452	0.93[AFR][1000 genomes]
rs880477	0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9817077	0.82[MKK][hapmap]
rs9817872	0.82[MKK][hapmap]
rs9819195	0.82[MKK][hapmap]
rs9829057	0.82[MKK][hapmap]
rs9880909	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv460534	chr3:51393046-51416108	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv590274	chr3:51393046-51416108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1480366	HEMK1	cis	lymphoblastoid	seeQTL
rs1480366	HEMK	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51378000-51399800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:51378600-51421000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:51378800-51421400	Weak transcription	Right Ventricle	heart
4	chr3:51379000-51393800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:51379000-51414600	Weak transcription	Left Ventricle	heart
6	chr3:51379200-51393600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:51379200-51393800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:51379200-51399800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:51379400-51403400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:51380000-51398400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:51380000-51398400	Weak transcription	Aorta	Aorta
12	chr3:51384200-51393800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:51384200-51420600	Weak transcription	Fetal Brain Male	brain
14	chr3:51385400-51405600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:51386400-51405400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:51388000-51393600	Weak transcription	Fetal Stomach	stomach
17	chr3:51388400-51400800	Strong transcription	Brain Angular Gyrus	brain
18	chr3:51390200-51400400	Strong transcription	Fetal Brain Female	brain
19	chr3:51390400-51394400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:51391000-51396600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:51391400-51393800	Weak transcription	Brain Hippocampus Middle	brain
22	chr3:51391600-51406800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:51391800-51393400	Weak transcription	Spleen	Spleen
24	chr3:51391800-51396600	Strong transcription	Stomach Smooth Muscle	stomach
25	chr3:51391800-51400400	Strong transcription	Brain Germinal Matrix	brain
26	chr3:51392000-51400600	Strong transcription	Brain Anterior Caudate	brain
27	chr3:51392200-51395000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:51392200-51395000	Enhancers	Esophagus	oesophagus
29	chr3:51392400-51393600	Enhancers	Gastric	stomach
30	chr3:51392400-51394000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:51392600-51393400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:51392600-51394400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:51392600-51395200	Enhancers	Stomach Mucosa	stomach
34	chr3:51392600-51395800	Strong transcription	Brain Substantia Nigra	brain
35	chr3:51392800-51395800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:51392800-51400800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:51392800-51418600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:51393000-51394400	Weak transcription	HSMMtube	muscle
39	chr3:51393000-51394600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:51393000-51396400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:51393000-51400800	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr3:51393200-51393800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:51393200-51394000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:51393200-51394000	Enhancers	HMEC	breast
45	chr3:51393200-51405600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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