Variant report

Variant	rs8038619
Chromosome Location	chr15:83698826-83698827
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	chr15:83697758..83699573-chr15:83735210..83737094,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263643	Chromatin interaction
ENSG00000064726	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10220725	1.00[ASN][1000 genomes]
rs17295457	1.00[ASN][1000 genomes]
rs28408839	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28429062	1.00[CEU][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28454771	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28463621	1.00[ASN][1000 genomes]
rs28479338	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28509292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28510490	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28540116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28569354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28570610	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28662361	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28707195	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28711332	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28755408	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28819476	1.00[ASN][1000 genomes]
rs28836869	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67634629	1.00[ASN][1000 genomes]
rs7169539	1.00[ASN][1000 genomes]
rs7170046	1.00[ASN][1000 genomes]
rs7173876	1.00[CEU][hapmap]
rs72755930	1.00[ASN][1000 genomes]
rs72755935	1.00[ASN][1000 genomes]
rs72755947	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72755962	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9919979	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

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
rs8038619	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	chr15:83681000-83700200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:83681000-83705000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:83681200-83710200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:83681600-83732000	Weak transcription	Stomach Mucosa	stomach
5	chr15:83682000-83708400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:83682200-83708600	Weak transcription	Fetal Heart	heart
7	chr15:83683000-83723000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr15:83683400-83726600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:83687000-83708200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:83687600-83701200	Weak transcription	Fetal Brain Female	brain
11	chr15:83687600-83709600	Weak transcription	Brain Angular Gyrus	brain
12	chr15:83688800-83708800	Weak transcription	Fetal Brain Male	brain
13	chr15:83689200-83705200	Weak transcription	Psoas Muscle	Psoas
14	chr15:83689400-83705000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr15:83689400-83708600	Weak transcription	NHEK	skin
16	chr15:83690000-83708200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:83690000-83708800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr15:83690400-83708000	Weak transcription	Brain Germinal Matrix	brain
19	chr15:83691600-83699000	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr15:83692000-83701200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:83692000-83702000	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:83692200-83700000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:83692200-83701000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:83692200-83701800	Strong transcription	Duodenum Mucosa	Duodenum
25	chr15:83692400-83699000	Strong transcription	A549	lung
26	chr15:83692400-83699200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr15:83692400-83702200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr15:83692600-83699200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr15:83693200-83699200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr15:83693200-83702200	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr15:83693200-83702800	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr15:83694600-83701800	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr15:83695000-83699000	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr15:83695000-83699200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
35	chr15:83695000-83699200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr15:83695000-83699200	Strong transcription	GM12878-XiMat	blood
37	chr15:83695000-83699400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:83695000-83699400	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr15:83695000-83701600	Strong transcription	Primary hematopoietic stem cells	blood
40	chr15:83695000-83703200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr15:83695000-83704000	Strong transcription	Primary B cells from peripheral blood	blood
42	chr15:83695000-83704200	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr15:83695400-83714600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr15:83695600-83699000	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:83695600-83699200	Strong transcription	Stomach Smooth Muscle	stomach
46	chr15:83695600-83699600	Strong transcription	Dnd41	blood
47	chr15:83695600-83702000	Strong transcription	Primary B cells from cord blood	blood
48	chr15:83695800-83699200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr15:83695800-83699200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr15:83695800-83699600	Strong transcription	Cortex derived primary cultured neurospheres	brain

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