Variant report

Variant	rs4681298
Chromosome Location	chr3:145844373-145844374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:145832521..145835172-chr3:145842139..145845404,4	MCF-7	breast:
2	chr3:145842696..145844403-chr3:145846645..145849074,2	MCF-7	breast:
3	chr3:145843855..145845524-chr3:145864168..145866252,2	MCF-7	breast:
4	chr3:145843180..145847334-chr3:145876555..145880843,5	MCF-7	breast:
5	chr3:145841131..145847641-chr3:145875218..145882802,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11928424	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs17412259	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2864795	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34803917	0.94[EUR][1000 genomes]
rs3762690	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3920230	1.00[YRI][hapmap]
rs4681295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681296	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780480	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]
rs73148913	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73148936	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73148944	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73148974	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73148977	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73148979	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73148981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73148992	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73148994	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73148996	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73148997	0.97[EUR][1000 genomes];0.83[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	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
2	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
3	nsv877613	chr3:145833232-145912055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4681298	PLOD2	Cis_1M	lymphoblastoid	RTeQTL
rs4681298	PLOD2	cis	lymphoblastoid	seeQTL
rs4681298	GFRAL	trans	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145784600-145848800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:145810400-145849800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:145810800-145851200	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:145819800-145849200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:145821000-145849800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:145827000-145855200	Weak transcription	Aorta	Aorta
7	chr3:145831400-145848400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:145832000-145870800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:145832600-145848400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:145834200-145851200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:145834400-145851400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:145834600-145852800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:145835200-145851200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:145835200-145852200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:145835600-145851200	Weak transcription	Fetal Kidney	kidney
16	chr3:145835800-145846000	Weak transcription	Fetal Intestine Small	intestine
17	chr3:145835800-145874000	Weak transcription	Psoas Muscle	Psoas
18	chr3:145836000-145852400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:145837000-145848800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:145837000-145852400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:145837200-145845800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:145837200-145846000	Weak transcription	Adipose Nuclei	Adipose
23	chr3:145837200-145846000	Weak transcription	Fetal Lung	lung
24	chr3:145837200-145851200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:145839200-145845200	Weak transcription	Colon Smooth Muscle	Colon
26	chr3:145839400-145847600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:145839800-145849000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:145839800-145851400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:145840000-145852400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:145840200-145847600	Weak transcription	HSMMtube	muscle
31	chr3:145840200-145849800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:145840400-145846000	Weak transcription	Fetal Intestine Large	intestine
33	chr3:145840400-145874000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:145840600-145845000	Weak transcription	Liver	Liver
35	chr3:145840600-145848600	Weak transcription	Fetal Stomach	stomach
36	chr3:145841800-145845000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:145842000-145846200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr3:145842000-145849800	Weak transcription	HMEC	breast
39	chr3:145842800-145845200	Enhancers	Osteobl	bone
40	chr3:145843000-145844800	Enhancers	Muscle Satellite Cultured Cells	--
41	chr3:145843200-145844400	Enhancers	NH-A	brain
42	chr3:145843200-145845200	Genic enhancers	HSMM	muscle
43	chr3:145843400-145848800	Weak transcription	Right Atrium	heart
44	chr3:145843400-145851200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr3:145843600-145848800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:145843600-145848800	Weak transcription	Ovary	ovary
47	chr3:145843600-145855200	Weak transcription	Left Ventricle	heart
48	chr3:145843600-145861200	Weak transcription	Right Ventricle	heart
49	chr3:145843800-145844400	Enhancers	Fetal Heart	heart
50	chr3:145843800-145844800	Enhancers	HUVEC	blood vessel

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