Variant report

Variant	rs2577540
Chromosome Location	chr5:128301742-128301743
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:128301330..128303294-chr5:128429299..128431386,3	K562	blood:
2	chr5:128299750..128303179-chr5:128428591..128431385,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066583	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs11740215	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs13166325	0.94[ASN][1000 genomes]
rs13169590	0.81[ASN][1000 genomes]
rs13190393	0.94[ASN][1000 genomes]
rs1421890	0.89[ASN][1000 genomes]
rs17616784	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17616974	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap]
rs17616991	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap]
rs1898543	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1898544	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1898549	0.94[ASN][1000 genomes]
rs2526196	0.94[ASN][1000 genomes]
rs2526201	0.94[ASN][1000 genomes]
rs2526202	0.94[ASN][1000 genomes]
rs2526209	0.94[ASN][1000 genomes]
rs2526210	0.94[ASN][1000 genomes]
rs2526211	0.94[ASN][1000 genomes]
rs2526212	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2526213	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2526214	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2526225	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2526239	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2526240	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2526241	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2526243	0.93[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2526245	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs2526247	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2526248	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap]
rs2526249	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap]
rs2526251	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs2526252	1.00[CHB][hapmap]
rs2526257	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap]
rs2545015	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2577399	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2577402	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2577403	0.94[ASN][1000 genomes]
rs2577429	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap]
rs2577436	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs2577445	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2577446	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2577477	0.80[ASN][1000 genomes]
rs2577504	0.94[ASN][1000 genomes]
rs2577506	0.94[ASN][1000 genomes]
rs2577507	0.94[ASN][1000 genomes]
rs2577508	0.94[ASN][1000 genomes]
rs2577509	0.94[ASN][1000 genomes]
rs2577510	0.94[ASN][1000 genomes]
rs2577511	0.94[ASN][1000 genomes]
rs2577512	0.94[ASN][1000 genomes]
rs2577513	0.94[ASN][1000 genomes]
rs2577514	0.94[ASN][1000 genomes]
rs2577528	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2577529	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2577530	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2577533	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.86[MKK][hapmap];0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2577534	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2577535	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2577536	0.95[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2577537	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2577538	1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2577539	0.88[JPT][hapmap]
rs2577541	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577542	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap]
rs2577543	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[MEX][hapmap]
rs2577545	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap]
rs2577546	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs2577555	0.94[ASN][1000 genomes]
rs2577556	0.94[ASN][1000 genomes]
rs2577560	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2577561	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2577562	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs34075274	0.94[ASN][1000 genomes]
rs34299037	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs34683252	0.94[ASN][1000 genomes]
rs34813132	0.94[ASN][1000 genomes]
rs34831887	0.94[ASN][1000 genomes]
rs35044703	0.94[ASN][1000 genomes]
rs35388070	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs35590597	0.83[ASN][1000 genomes]
rs35696888	0.94[ASN][1000 genomes]
rs35767068	0.94[ASN][1000 genomes]
rs36147677	0.80[ASN][1000 genomes]
rs62391271	0.94[ASN][1000 genomes]
rs62391272	0.94[ASN][1000 genomes]
rs62391297	0.91[ASN][1000 genomes]
rs71587998	0.91[ASN][1000 genomes]
rs71592877	0.91[ASN][1000 genomes]
rs7349831	0.94[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	nsv882839	chr5:128205828-128390167	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv882840	chr5:128205828-128428962	Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830485	chr5:128298622-128480492	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv819884	chr5:128301059-128303254	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2577540	SLC27A6	cis	cerebellum	SCAN
rs2577540	CCNI2	cis	cerebellum	SCAN
rs2577540	SLC27A6	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:128300400-128301800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:128300400-128301800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:128300400-128301800	Active TSS	Brain Substantia Nigra	brain
4	chr5:128300400-128301800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr5:128300400-128302000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr5:128300400-128302000	Active TSS	K562	blood
7	chr5:128300400-128302200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr5:128300400-128302200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr5:128300400-128302200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
10	chr5:128300400-128302200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr5:128300600-128301800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:128300600-128301800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:128300600-128301800	Bivalent/Poised TSS	Fetal Brain Female	brain
14	chr5:128300600-128302000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:128300600-128302000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr5:128300600-128302000	Active TSS	Thymus	Thymus
17	chr5:128300600-128302200	Active TSS	Placenta Amnion	Placenta Amnion
18	chr5:128300600-128302400	Active TSS	Ovary	ovary
19	chr5:128300600-128303000	Active TSS	Left Ventricle	heart
20	chr5:128300600-128303200	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr5:128300600-128303200	Active TSS	Right Atrium	heart
22	chr5:128300600-128303600	Active TSS	Right Ventricle	heart
23	chr5:128300800-128301800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
24	chr5:128300800-128301800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:128300800-128302000	Bivalent/Poised TSS	Fetal Stomach	stomach
26	chr5:128300800-128302200	Active TSS	Rectal Mucosa Donor 31	rectum
27	chr5:128301000-128301800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
28	chr5:128301000-128301800	Active TSS	Gastric	stomach
29	chr5:128301200-128301800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr5:128301200-128301800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr5:128301200-128301800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
32	chr5:128301200-128302000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
33	chr5:128301200-128302000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
34	chr5:128301400-128301800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
35	chr5:128301400-128301800	Flanking Active TSS	Esophagus	oesophagus
36	chr5:128301400-128301800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
37	chr5:128301400-128302000	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr5:128301400-128302400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:128301400-128302600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:128301600-128301800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr5:128301600-128301800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
42	chr5:128301600-128301800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
43	chr5:128301600-128301800	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:128301600-128301800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr5:128301600-128301800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
46	chr5:128301600-128301800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:128301600-128301800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr5:128301600-128301800	Bivalent Enhancer	Adipose Nuclei	Adipose
49	chr5:128301600-128301800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
50	chr5:128301600-128301800	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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