Variant report

Variant	rs12973764
Chromosome Location	chr19:44023153-44023154
allele	G/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: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12980646	1.00[ASW][hapmap];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];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12981023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs184239	0.89[CEU][hapmap]
rs2102954	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs2682585	0.89[CEU][hapmap]
rs2682586	0.89[CEU][hapmap];0.86[MEX][hapmap]
rs2854501	0.91[ASW][hapmap];0.88[MEX][hapmap]
rs2854506	0.84[CEU][hapmap];0.86[MEX][hapmap]
rs2854508	0.84[CEU][hapmap]
rs2854509	0.84[CEU][hapmap];0.86[MEX][hapmap]
rs304731	0.87[CEU][hapmap];0.91[YRI][hapmap]
rs3213334	0.88[MEX][hapmap]
rs4802183	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4802185	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7248167	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap]
rs7253856	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap]
rs762506	0.84[CEU][hapmap];0.86[MEX][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12973764	LOC653583///PHLDB3	Cis_1M	lymphoblastoid	RTeQTL
rs12973764	ETHE1	Cis_1M	lymphoblastoid	RTeQTL
rs12973764	BLOC1S3	cis	parietal	SCAN
rs12973764	ETHE1	cis	lymphoblastoid	seeQTL
rs12973764	KCNJ14	cis	cerebellum	SCAN

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	chr19:44010400-44023400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr19:44010400-44023600	Weak transcription	K562	blood
11	chr19:44011200-44029400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr19:44013000-44028600	Weak transcription	Colon Smooth Muscle	Colon
13	chr19:44013000-44028800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr19:44013200-44023400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr19:44013200-44028600	Weak transcription	Brain Hippocampus Middle	brain
16	chr19:44013200-44029800	Weak transcription	Small Intestine	intestine
17	chr19:44013400-44023800	Weak transcription	Fetal Lung	lung
18	chr19:44013400-44029400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr19:44013600-44023600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:44014400-44023200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:44014400-44023400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr19:44014400-44029400	Weak transcription	Dnd41	blood
23	chr19:44015200-44028600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr19:44015200-44028800	Weak transcription	Gastric	stomach
25	chr19:44015400-44023400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr19:44015400-44023600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:44015400-44028400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr19:44015400-44028800	Weak transcription	Fetal Thymus	thymus
29	chr19:44015400-44028800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr19:44015400-44029000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:44015400-44029200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr19:44015400-44029400	Weak transcription	Brain Germinal Matrix	brain
33	chr19:44015400-44029600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr19:44015600-44023200	Weak transcription	Osteobl	bone
35	chr19:44015600-44023400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr19:44015600-44023400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr19:44015600-44023600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr19:44015600-44023600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr19:44015600-44027000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr19:44015600-44027000	Weak transcription	A549	lung
41	chr19:44015600-44028400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr19:44015600-44028600	Weak transcription	Adipose Nuclei	Adipose
43	chr19:44015600-44028800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr19:44015600-44028800	Weak transcription	HepG2	liver
45	chr19:44015600-44029400	Weak transcription	Brain Anterior Caudate	brain
46	chr19:44015600-44029600	Weak transcription	Brain Substantia Nigra	brain
47	chr19:44015800-44023400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr19:44015800-44023400	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr19:44015800-44023400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr19:44015800-44023600	Weak transcription	Liver	Liver

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