Variant report

Variant	rs3213387
Chromosome Location	chr19:44052616-44052617
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr19:44052459-44052935	K562	blood:	n/a	n/a
2	NR2F2	chr19:44052472-44052836	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44050644..44056032-chr19:44057547..44060902,6	K562	blood:
2	chr19:44051958..44054439-chr19:44057547..44062294,4	K562	blood:
3	chr19:44049826..44052731-chr19:44057585..44060177,2	MCF-7	breast:
4	chr19:44036171..44040014-chr19:44052503..44054920,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269177	TF binding region
ENSG00000176472	Chromatin interaction
ENSG00000269177	Chromatin interaction
ENSG00000073050	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12981701	0.96[ASN][1000 genomes]
rs12983281	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1475933	1.00[ASN][1000 genomes]
rs184239	0.83[ASN][1000 genomes]
rs1978008	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2030404	0.95[ASN][1000 genomes]
rs2139720	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs25479	1.00[ASN][1000 genomes]
rs25485	0.95[ASN][1000 genomes]
rs2599461	0.95[ASN][1000 genomes]
rs2599462	0.98[ASN][1000 genomes]
rs2682561	0.91[ASN][1000 genomes]
rs2682563	0.96[ASN][1000 genomes]
rs2682585	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2854500	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2854501	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2854506	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2854507	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2854508	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2854509	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs304731	0.83[ASN][1000 genomes]
rs3213255	0.82[ASN][1000 genomes]
rs3213263	0.82[ASN][1000 genomes]
rs3213276	0.84[ASN][1000 genomes]
rs3213295	0.82[EUR][1000 genomes]
rs3213329	0.90[ASN][1000 genomes]
rs3213333	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3213334	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3213356	0.93[ASN][1000 genomes]
rs3547	1.00[ASN][1000 genomes]
rs56012842	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73043690	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762506	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs762507	0.95[ASN][1000 genomes]
rs915927	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
13	nsv912107	chr19:44030998-44055726	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3213387	ETHE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44038600-44054000	Weak transcription	Psoas Muscle	Psoas
2	chr19:44038800-44055800	Weak transcription	Stomach Mucosa	stomach
3	chr19:44039200-44078600	Weak transcription	Hela-S3	cervix
4	chr19:44040800-44060800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr19:44041800-44065200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:44042400-44058000	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr19:44043200-44064600	Weak transcription	NHDF-Ad	bronchial
8	chr19:44043400-44058800	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr19:44043400-44059000	Strong transcription	Fetal Muscle Trunk	muscle
10	chr19:44043400-44059200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:44043600-44054600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr19:44043600-44057800	Strong transcription	Stomach Smooth Muscle	stomach
13	chr19:44043600-44059200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr19:44043600-44065800	Strong transcription	Adipose Nuclei	Adipose
15	chr19:44043800-44065800	Weak transcription	Fetal Heart	heart
16	chr19:44043800-44074000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr19:44044600-44069000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:44045200-44062800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:44046200-44056800	Weak transcription	Fetal Brain Male	brain
20	chr19:44047400-44052800	Weak transcription	K562	blood
21	chr19:44047400-44066600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:44048000-44054200	Weak transcription	HepG2	liver
23	chr19:44048000-44055600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr19:44048200-44053200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr19:44048200-44055800	Weak transcription	Fetal Kidney	kidney
26	chr19:44048200-44062000	Weak transcription	NH-A	brain
27	chr19:44048200-44067000	Weak transcription	HUVEC	blood vessel
28	chr19:44048400-44053200	Weak transcription	A549	lung
29	chr19:44048400-44054400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr19:44048400-44054400	Weak transcription	HMEC	breast
31	chr19:44048400-44078800	Weak transcription	Small Intestine	intestine
32	chr19:44048600-44053400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr19:44048600-44055400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr19:44048800-44054600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr19:44049200-44053400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr19:44049400-44053000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr19:44049400-44054400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr19:44049600-44054600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr19:44049800-44054200	Weak transcription	Colon Smooth Muscle	Colon
40	chr19:44049800-44054200	Weak transcription	Left Ventricle	heart
41	chr19:44049800-44054200	Weak transcription	HSMMtube	muscle
42	chr19:44049800-44054600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr19:44049800-44055600	Weak transcription	Pancreas	Pancrea
44	chr19:44050000-44053000	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr19:44050000-44053600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:44050000-44054000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr19:44050000-44054000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr19:44050000-44054600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr19:44050000-44054800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr19:44050200-44054000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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