Variant report

Variant	rs3872609
Chromosome Location	chr3:112727462-112727463
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112727442..112729984-chr3:112737783..112739677,2	MCF-7	breast:
2	chr3:112709111..112712767-chr3:112725826..112728376,3	K562	blood:
3	chr3:112726403..112732813-chr3:112735056..112739637,9	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD200R1-1	chr3:112727018-112727647	NONHSAT091203

Variant related genes	Relation type
ENSG00000240057	Chromatin interaction
ENSG00000272844	Chromatin interaction
ENSG00000163607	Chromatin interaction
ENSG00000163608	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10460813	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1110819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1488191	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1809629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2399434	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2399460	0.81[CHB][hapmap]
rs3872610	0.91[CEU][hapmap]
rs57720936	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650483	0.85[CHB][hapmap]
rs983386	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs984706	0.93[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.93[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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv1843165	chr3:112628205-112740145	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3872609	GTPBP8	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112710400-112737400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:112711400-112736600	Weak transcription	Stomach Mucosa	stomach
3	chr3:112712200-112736800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:112712400-112736600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:112712800-112736600	Weak transcription	Fetal Heart	heart
6	chr3:112714400-112736800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:112715000-112735800	Strong transcription	Primary B cells from cord blood	blood
8	chr3:112715200-112736000	Strong transcription	Primary hematopoietic stem cells	blood
9	chr3:112715600-112734600	Strong transcription	Liver	Liver
10	chr3:112715600-112736600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:112715600-112736600	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:112715800-112735800	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr3:112715800-112736000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:112715800-112736200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:112715800-112736800	Strong transcription	Placenta	Placenta
16	chr3:112716000-112736000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr3:112716000-112736600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr3:112716200-112735800	Strong transcription	A549	lung
19	chr3:112716400-112735600	Strong transcription	Adipose Nuclei	Adipose
20	chr3:112716400-112736400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:112716400-112736400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:112716800-112729200	Strong transcription	Fetal Lung	lung
23	chr3:112716800-112734400	Strong transcription	GM12878-XiMat	blood
24	chr3:112716800-112735800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:112716800-112736200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr3:112716800-112736400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:112716800-112736400	Strong transcription	NH-A	brain
28	chr3:112716800-112736600	Strong transcription	Osteobl	bone
29	chr3:112716800-112736800	Strong transcription	HSMM	muscle
30	chr3:112717000-112729600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:112717000-112729600	Strong transcription	Fetal Intestine Large	intestine
32	chr3:112717000-112736400	Strong transcription	Primary B cells from peripheral blood	blood
33	chr3:112717200-112728000	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:112717200-112736000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:112717200-112736200	Strong transcription	HMEC	breast
36	chr3:112717400-112733200	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr3:112718400-112736200	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr3:112718600-112728000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:112718600-112729400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:112718600-112735800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:112719600-112728000	Strong transcription	Hela-S3	cervix
42	chr3:112719800-112729600	Strong transcription	Brain Anterior Caudate	brain
43	chr3:112720000-112727800	Strong transcription	HUVEC	blood vessel
44	chr3:112720000-112736400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:112720400-112730000	Strong transcription	Fetal Kidney	kidney
46	chr3:112720800-112729800	Strong transcription	Fetal Muscle Leg	muscle
47	chr3:112721000-112729600	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:112721000-112729800	Strong transcription	HepG2	liver
49	chr3:112721200-112728600	Strong transcription	Fetal Muscle Trunk	muscle
50	chr3:112721400-112728400	Strong transcription	Fetal Brain Male	brain

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