Variant report

Variant	rs6780480
Chromosome Location	chr3:145825043-145825044
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	chr3:145820162..145825739-chr3:145873098..145880384,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11928424	1.00[JPT][hapmap]
rs17412259	1.00[AFR][1000 genomes]
rs2864795	0.81[EUR][1000 genomes]
rs3762690	0.81[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3920230	1.00[YRI][hapmap]
rs4681295	0.81[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4681296	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4681298	0.81[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4681300	1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs58957322	0.94[ASN][1000 genomes]
rs73148913	1.00[AFR][1000 genomes]
rs73148936	1.00[AFR][1000 genomes]
rs73148944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73148974	0.84[EUR][1000 genomes]
rs73148977	0.83[EUR][1000 genomes]
rs73148979	0.82[EUR][1000 genomes]
rs73148981	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs73148992	0.83[EUR][1000 genomes]
rs73148994	0.83[EUR][1000 genomes]
rs73148996	0.83[EUR][1000 genomes]
rs73148997	0.83[EUR][1000 genomes]
rs73150815	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877584	chr3:144903957-145833232	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv525829	chr3:145614317-145863779	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv4046	chr3:145693249-145880189	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6780480	PLOD2	Cis_1M	lymphoblastoid	RTeQTL
rs6780480	PLOD2	cis	lymphoblastoid	seeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145781800-145831800	Weak transcription	Psoas Muscle	Psoas
2	chr3:145782800-145843200	Weak transcription	Pancreas	Pancrea
3	chr3:145784600-145848800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:145789200-145830800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:145790400-145843200	Weak transcription	Right Ventricle	heart
6	chr3:145791600-145833800	Weak transcription	NHDF-Ad	bronchial
7	chr3:145794400-145827000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:145794400-145828000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:145798800-145839200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:145808600-145833000	Weak transcription	Fetal Lung	lung
11	chr3:145810400-145829000	Weak transcription	NHLF	lung
12	chr3:145810400-145830800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:145810400-145849800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:145810600-145827200	Weak transcription	Small Intestine	intestine
15	chr3:145810800-145851200	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:145812000-145826000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:145812000-145826800	Weak transcription	Aorta	Aorta
18	chr3:145812200-145839200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:145814200-145841000	Weak transcription	Lung	lung
20	chr3:145814600-145828200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:145815600-145825200	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr3:145815600-145825400	Strong transcription	HSMM	muscle
23	chr3:145815800-145830000	Strong transcription	Osteobl	bone
24	chr3:145816000-145836800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:145816400-145842000	Weak transcription	Colonic Mucosa	Colon
26	chr3:145818000-145825600	Weak transcription	Fetal Intestine Small	intestine
27	chr3:145818000-145827400	Strong transcription	Fetal Intestine Large	intestine
28	chr3:145818000-145829800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:145818600-145827200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:145818800-145831600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr3:145819000-145829200	Weak transcription	Fetal Muscle Leg	muscle
32	chr3:145819200-145828400	Strong transcription	NH-A	brain
33	chr3:145819800-145826800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:145819800-145831200	Weak transcription	Fetal Stomach	stomach
35	chr3:145819800-145841800	Weak transcription	Fetal Heart	heart
36	chr3:145819800-145849200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr3:145820000-145834000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:145820600-145830000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:145821000-145830800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:145821000-145831600	Weak transcription	Placenta	Placenta
41	chr3:145821000-145849800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:145821200-145826800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:145821200-145835200	Weak transcription	Colon Smooth Muscle	Colon
44	chr3:145821200-145835400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr3:145821600-145826600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:145821800-145826000	Weak transcription	Left Ventricle	heart
47	chr3:145822000-145826600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr3:145822000-145829600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr3:145822200-145826400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr3:145822200-145833800	Weak transcription	Fetal Kidney	kidney

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