Variant report

Variant	rs34977009
Chromosome Location	chr19:44022663-44022664
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	chr19:44007109..44009173-chr19:44021498..44024466,3	MCF-7	breast:
2	chr19:43967016..43970562-chr19:44022266..44025437,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124466	Chromatin interaction
ENSG00000176531	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12460021	0.84[EUR][1000 genomes]
rs12979907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12980646	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12981023	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs184239	0.81[EUR][1000 genomes]
rs1978008	0.80[EUR][1000 genomes]
rs2102954	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2682585	0.82[EUR][1000 genomes]
rs2854506	0.81[EUR][1000 genomes]
rs2854507	0.80[EUR][1000 genomes]
rs2854508	0.81[EUR][1000 genomes]
rs2854509	0.81[EUR][1000 genomes]
rs304731	0.81[EUR][1000 genomes]
rs3213295	0.80[EUR][1000 genomes]
rs3213391	0.84[EUR][1000 genomes]
rs35016410	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35485252	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36075334	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3810381	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4507015	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4544340	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802183	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4802185	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59000923	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59827264	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61607741	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6509094	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71362654	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7248927	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7252962	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7253177	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs762506	0.81[EUR][1000 genomes]
rs8100211	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1056785	chr19:44010370-44081601	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34977009	ETHE1	Cis_1M	lymphoblastoid	RTeQTL
rs34977009	LOC653583///PHLDB3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44009000-44023600	Weak transcription	Stomach Mucosa	stomach
2	chr19:44009200-44029200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:44009200-44029600	Weak transcription	Psoas Muscle	Psoas
4	chr19:44009400-44023600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:44009600-44023400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr19:44009600-44023600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr19:44009600-44023600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr19:44010200-44023400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr19:44010400-44023000	Weak transcription	Hela-S3	cervix
10	chr19:44010400-44023400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:44010400-44023600	Weak transcription	K562	blood
12	chr19:44011200-44029400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr19:44013000-44028600	Weak transcription	Colon Smooth Muscle	Colon
14	chr19:44013000-44028800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:44013200-44023400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr19:44013200-44028600	Weak transcription	Brain Hippocampus Middle	brain
17	chr19:44013200-44029800	Weak transcription	Small Intestine	intestine
18	chr19:44013400-44023000	Weak transcription	NH-A	brain
19	chr19:44013400-44023800	Weak transcription	Fetal Lung	lung
20	chr19:44013400-44029400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr19:44013600-44023600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr19:44014400-44023200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:44014400-44023400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr19:44014400-44029400	Weak transcription	Dnd41	blood
25	chr19:44015000-44023000	Weak transcription	HSMMtube	muscle
26	chr19:44015200-44028600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr19:44015200-44028800	Weak transcription	Gastric	stomach
28	chr19:44015400-44023400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr19:44015400-44023600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr19:44015400-44028400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr19:44015400-44028800	Weak transcription	Fetal Thymus	thymus
32	chr19:44015400-44028800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr19:44015400-44029000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:44015400-44029200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr19:44015400-44029400	Weak transcription	Brain Germinal Matrix	brain
36	chr19:44015400-44029600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr19:44015600-44023000	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr19:44015600-44023000	Weak transcription	GM12878-XiMat	blood
39	chr19:44015600-44023200	Weak transcription	Osteobl	bone
40	chr19:44015600-44023400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr19:44015600-44023400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr19:44015600-44023600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr19:44015600-44023600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr19:44015600-44027000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:44015600-44027000	Weak transcription	A549	lung
46	chr19:44015600-44028400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr19:44015600-44028600	Weak transcription	Adipose Nuclei	Adipose
48	chr19:44015600-44028800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr19:44015600-44028800	Weak transcription	HepG2	liver
50	chr19:44015600-44029400	Weak transcription	Brain Anterior Caudate	brain

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