Variant report

Variant	rs579270
Chromosome Location	chr13:39990356-39990357
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	chr13:39989312..39990379-chr13:40174545..40175487,4	MCF-7	breast:
2	chr13:39989718..39990375-chr15:56538148..56538851,2	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10492738	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11147763	0.88[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17059863	0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6563702	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1036674	chr13:39841482-40008117	Bivalent Enhancer Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv900008	chr13:39962791-40020267	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs579270	LHFP	cis	lymphoblastoid	seeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39976600-39990600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr13:39981400-39991800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr13:39981400-39991800	Weak transcription	NHEK	skin
4	chr13:39984200-39991200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr13:39984600-39991400	Weak transcription	NH-A	brain
6	chr13:39984800-39991400	Weak transcription	NHLF	lung
7	chr13:39985000-39990400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr13:39985000-39991200	Weak transcription	HSMM	muscle
9	chr13:39986000-39991200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr13:39986000-39991400	Weak transcription	Right Ventricle	heart
11	chr13:39986200-39991000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr13:39986800-39992000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr13:39988600-39991200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:39988600-39991600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr13:39988600-39992200	Enhancers	Fetal Stomach	stomach
16	chr13:39988600-39994600	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr13:39988600-39995000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr13:39988800-39994600	Enhancers	Fetal Heart	heart
19	chr13:39989000-39991200	Enhancers	Brain Anterior Caudate	brain
20	chr13:39989000-39991600	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr13:39989200-39991400	Enhancers	NHDF-Ad	bronchial
22	chr13:39989400-39991200	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr13:39989400-39991200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr13:39989400-39993400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr13:39989600-39990600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr13:39989600-39990800	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr13:39989600-39991200	Weak transcription	HSMMtube	muscle
28	chr13:39989600-39991400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr13:39989600-39991400	Enhancers	Brain Cingulate Gyrus	brain
30	chr13:39989600-39993400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr13:39989800-39990400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr13:39989800-39991400	Weak transcription	Aorta	Aorta
33	chr13:39989800-39991400	Enhancers	Brain Hippocampus Middle	brain
34	chr13:39989800-39991600	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr13:39989800-39991600	Weak transcription	GM12878-XiMat	blood
36	chr13:39989800-39991800	Enhancers	Colon Smooth Muscle	Colon
37	chr13:39989800-39992000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr13:39990000-39991000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr13:39990000-39991200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr13:39990000-39991200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr13:39990000-39991200	Weak transcription	Fetal Muscle Leg	muscle
42	chr13:39990000-39991200	Weak transcription	Right Atrium	heart
43	chr13:39990000-39991400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr13:39990000-39991400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr13:39990000-39991400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr13:39990000-39991400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr13:39990000-39991400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr13:39990000-39991400	Weak transcription	Left Ventricle	heart
49	chr13:39990000-39991400	Enhancers	Rectal Smooth Muscle	rectum
50	chr13:39990000-39991600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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