Variant report

Variant	rs4079029
Chromosome Location	chr15:83727830-83727831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83718422..83721272-chr15:83727802..83729791,2	MCF-7	breast:
2	chr15:83726826..83729671-chr15:83873975..83877192,5	MCF-7	breast:
3	chr15:83723627..83726592-chr15:83727241..83728963,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000064726	Chromatin interaction
ENSG00000166503	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10400812	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10520576	1.00[JPT][hapmap]
rs1112404	1.00[JPT][hapmap]
rs11259965	1.00[JPT][hapmap]
rs11259969	1.00[JPT][hapmap]
rs11852408	1.00[JPT][hapmap]
rs11852496	1.00[JPT][hapmap]
rs11853742	0.91[JPT][hapmap]
rs11856171	1.00[JPT][hapmap]
rs11857428	1.00[JPT][hapmap]
rs11857641	1.00[JPT][hapmap]
rs11858074	0.95[ASN][1000 genomes]
rs11858377	1.00[JPT][hapmap]
rs12440386	1.00[JPT][hapmap]
rs12441585	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs12443109	1.00[JPT][hapmap]
rs12591855	1.00[JPT][hapmap]
rs12592391	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12593316	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs12593638	0.91[JPT][hapmap]
rs12594496	1.00[JPT][hapmap]
rs12595330	1.00[JPT][hapmap]
rs12899522	0.92[ASN][1000 genomes]
rs12900411	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12901811	0.95[ASN][1000 genomes]
rs12902721	0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12903066	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12904695	0.97[ASN][1000 genomes]
rs12906027	0.95[ASN][1000 genomes]
rs12906626	0.97[ASN][1000 genomes]
rs12907032	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12911706	0.95[ASN][1000 genomes]
rs12911891	0.95[ASN][1000 genomes]
rs12913130	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12917594	0.97[ASN][1000 genomes]
rs13329195	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13329269	0.92[ASN][1000 genomes]
rs17158080	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs17158127	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17294476	0.90[JPT][hapmap]
rs17507300	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17567151	1.00[JPT][hapmap]
rs17567869	1.00[JPT][hapmap]
rs17568459	1.00[JPT][hapmap]
rs2034617	0.91[JPT][hapmap]
rs2034618	1.00[JPT][hapmap]
rs2084839	0.88[ASN][1000 genomes]
rs2381030	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs28436027	0.91[JPT][hapmap]
rs28485801	0.97[ASN][1000 genomes]
rs28580677	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087804	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs34869943	0.92[ASN][1000 genomes]
rs35207081	0.95[ASN][1000 genomes]
rs35627116	0.97[ASN][1000 genomes]
rs36038412	0.95[ASN][1000 genomes]
rs4563011	1.00[JPT][hapmap]
rs6603044	0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs6603046	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6603047	0.91[JPT][hapmap]
rs66606849	0.95[ASN][1000 genomes]
rs67482297	0.95[ASN][1000 genomes]
rs67822554	0.95[ASN][1000 genomes]
rs7163516	0.94[ASN][1000 genomes]
rs7164083	0.82[JPT][hapmap]
rs7165114	1.00[JPT][hapmap]
rs7165978	1.00[JPT][hapmap]
rs7166645	0.98[ASN][1000 genomes]
rs7170547	0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7172665	0.87[ASW][hapmap];0.92[GIH][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs7177599	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7180407	1.00[JPT][hapmap]
rs7181169	0.97[ASN][1000 genomes]
rs7495911	1.00[JPT][hapmap]
rs750214	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7757	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8023669	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs8027193	1.00[JPT][hapmap]
rs8027577	1.00[JPT][hapmap]
rs8031896	0.98[ASN][1000 genomes]
rs8035810	1.00[JPT][hapmap]
rs8037783	1.00[JPT][hapmap]
rs8038486	1.00[JPT][hapmap]
rs8040457	0.98[ASN][1000 genomes]
rs8040998	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs8043224	1.00[JPT][hapmap]
rs9646239	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs965264	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040336	chr15:83578947-83768335	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv482308	chr15:83584918-83747362	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4079029	HDGFRP3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83681600-83732000	Weak transcription	Stomach Mucosa	stomach
2	chr15:83700400-83734400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:83701600-83732800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:83705000-83731000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr15:83709600-83730800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr15:83710600-83730200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:83710600-83730200	Weak transcription	Esophagus	oesophagus
8	chr15:83714200-83730200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:83717400-83731400	Weak transcription	Spleen	Spleen
10	chr15:83718000-83731000	Weak transcription	Colonic Mucosa	Colon
11	chr15:83719800-83729800	Weak transcription	NHEK	skin
12	chr15:83720000-83729800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:83720400-83728600	Strong transcription	GM12878-XiMat	blood
14	chr15:83720800-83728600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr15:83722400-83730200	Weak transcription	HSMMtube	muscle
16	chr15:83722600-83730200	Weak transcription	NHDF-Ad	bronchial
17	chr15:83722600-83732800	Weak transcription	NHLF	lung
18	chr15:83722800-83730200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr15:83723400-83729600	Weak transcription	Fetal Kidney	kidney
20	chr15:83723800-83729800	Weak transcription	HMEC	breast
21	chr15:83724800-83729800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr15:83724800-83729800	Weak transcription	A549	lung
23	chr15:83724800-83729800	Weak transcription	Hela-S3	cervix
24	chr15:83724800-83730200	Weak transcription	Lung	lung
25	chr15:83724800-83730600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr15:83724800-83730600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr15:83724800-83731000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:83724800-83731400	Weak transcription	Brain Germinal Matrix	brain
29	chr15:83725000-83729800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr15:83725000-83733800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr15:83725200-83728000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:83725200-83728600	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr15:83725200-83730000	Weak transcription	HUVEC	blood vessel
34	chr15:83725200-83730200	Weak transcription	NH-A	brain
35	chr15:83725200-83730200	Weak transcription	Osteobl	bone
36	chr15:83725200-83732200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr15:83725200-83732200	Weak transcription	Thymus	Thymus
38	chr15:83725200-83732400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:83725400-83729800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr15:83725400-83729800	Weak transcription	Liver	Liver
41	chr15:83725400-83730400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:83725400-83730600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr15:83725400-83730600	Weak transcription	Adipose Nuclei	Adipose
44	chr15:83725400-83731200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr15:83725400-83734600	Weak transcription	Placenta	Placenta
46	chr15:83725600-83734400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr15:83725800-83728600	Enhancers	Right Ventricle	heart
48	chr15:83725800-83729600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr15:83726000-83729800	Weak transcription	Primary B cells from peripheral blood	blood
50	chr15:83726000-83729800	Weak transcription	Brain Substantia Nigra	brain

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