Variant report

Variant	rs4802183
Chromosome Location	chr19:44009364-44009365
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZBTB7A	chr19:44007805-44009365	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr19:44007991-44009542	HUVEC	blood vessel:	n/a	n/a
3	MTA3	chr19:44008436-44009482	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:44007504-44009435	HepG2	liver:	n/a	n/a
5	ZBTB7A	chr19:44007859-44009420	ECC-1	luminal epithelium:	n/a	chr19:44009356-44009370
6	GABPA	chr19:44008159-44009401	MCF-7	breast:	n/a	chr19:44008313-44008322
7	ELF1	chr19:44007821-44009402	GM12878	blood:	n/a	chr19:44008959-44008972 chr19:44008961-44008972 chr19:44008962-44008971 chr19:44008443-44008455 chr19:44008961-44008972
8	NR2F2	chr19:44008303-44009543	MCF-7	breast:	n/a	n/a
9	POLR2A	chr19:44008928-44009409	PFSK-1	brain:	n/a	n/a
10	MAZ	chr19:44007618-44009470	IMR90	lung:	n/a	chr19:44008970-44008980

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:44009353-44009403	AG09309	skin:	n/a
2	chr19:44009353-44009403	H1-hESC	embryonic stem cell:	embryo
3	chr19:44009353-44009403	HEK293	kidney:	embryo
4	chr19:44009353-44009403	HEEpiC	esophagus:	n/a
5	chr19:44009353-44009403	NHBE	bronchial:	n/a
6	chr19:44009353-44009403	HCM	heart:	n/a
7	chr19:44009353-44009403	HRPEpiC	eye:	n/a
8	chr19:44009353-44009403	HCPEpiC	choroid plexus:	n/a
9	chr19:44009353-44009403	GM12892	blood:	n/a
10	chr19:44009353-44009403	HepG2	liver:	n/a
11	chr19:44009353-44009403	AG04450	lung:	fetal
12	chr19:44009353-44009403	K562	blood:	n/a
13	chr19:44009353-44009403	HUVEC	blood vessel:	n/a
14	chr19:44009353-44009403	Caco-2	colon:	n/a
15	chr19:44009353-44009403	T-47D	breast:	n/a
16	chr19:44009353-44009403	PFSK-1	brain:	n/a
17	chr19:44009353-44009403	NT2-D1	testis:	n/a
18	chr19:44009353-44009403	SAEC	small airway:	n/a
19	chr19:44009353-44009403	SK-N-MC	brain:	n/a
20	chr19:44009353-44009403	GM06990	blood:	n/a
21	chr19:44009353-44009403	HIPEpiC	eye:	n/a
22	chr19:44009353-44009403	PrEC	prostate:	n/a
23	chr19:44009353-44009403	NB4	blood:	n/a
24	chr19:44009353-44009403	ProgFib	skin:	n/a
25	chr19:44009353-44009403	MCF10A-Er-Src	breast:	n/a
26	chr19:44009353-44009403	NHDF-neo	bronchial:	n/a
27	chr19:44009353-44009403	HRE	kidney:	n/a
28	chr19:44009353-44009403	GM12891	blood:	n/a
29	chr19:44009353-44009403	HMEC	breast:	n/a
30	chr19:44009353-44009403	AG04449	skin:	fetal
31	chr19:44009353-44009403	AG10803	skin:	n/a
32	chr19:44009353-44009403	SK-N-SH_RA	brain:	n/a
33	chr19:44009353-44009403	AG09319	gingival:	n/a
34	chr19:44009353-44009403	AoSMC	blood vessel:	n/a
35	chr19:44009353-44009403	HRCEpiC	kidney:	n/a
36	chr19:44009353-44009403	HAEpiC	amniotic membrane:	n/a
37	chr19:44009353-44009403	HPAEpiC	pulmonary alveolar:	n/a
38	chr19:44009353-44009403	ECC-1	luminal epithelium:	n/a
39	chr19:44009353-44009403	BE2_C	brain:	n/a
40	chr19:44009353-44009403	ovcar-3	ovarian:	n/a
41	chr19:44009353-44009403	GM19239	blood:	n/a
42	chr19:44009353-44009403	HCT-116	colon:	n/a
43	chr19:44009353-44009403	GM12878	blood:	n/a
44	chr19:44009353-44009403	BJ	skin:	n/a
45	chr19:44009353-44009403	U87	brain:	n/a
46	chr19:44009353-44009403	SKMC	muscle:	n/a
47	chr19:44009353-44009403	Hela-S3	cervix:	n/a
48	chr19:44009353-44009403	A549	lung:	n/a
49	chr19:44009353-44009403	LNCaP	prostate:	n/a
50	chr19:44009353-44009403	CMK	blood:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:43997566..43999974-chr19:44006795..44009700,2	K562	blood:
2	chr19:43967204..43969877-chr19:44006593..44010322,9	MCF-7	breast:
3	chr19:43966113..43971089-chr19:44005040..44010546,6	K562	blood:
4	chr19:44007568..44009583-chr19:44036201..44039639,3	MCF-7	breast:
5	chr19:43965066..43971111-chr19:44006791..44009897,14	MCF-7	breast:
6	chr19:44006689..44009864-chr19:44027261..44031051,4	MCF-7	breast:
7	chr19:43966525..43969059-chr19:44008556..44010178,2	K562	blood:

No data

Variant related genes	Relation type
PHLDB3	TF binding region
PHLDB3	CpG island
ENSG00000124466	Chromatin interaction
ENSG00000176531	Chromatin interaction
ENSG00000176472	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12460021	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12973764	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]
rs12979907	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12980646	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12981023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
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];0.84[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs2682585	0.89[CEU][hapmap]
rs2682586	0.89[CEU][hapmap]
rs2854501	0.91[ASW][hapmap]
rs2854506	0.84[CEU][hapmap]
rs2854508	0.84[CEU][hapmap]
rs2854509	0.84[CEU][hapmap]
rs304731	0.87[CEU][hapmap];0.91[YRI][hapmap]
rs34352751	0.80[EUR][1000 genomes]
rs34977009	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35016410	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35485252	0.87[EUR][1000 genomes]
rs36034157	0.81[EUR][1000 genomes]
rs36075334	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3810381	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4507015	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4544340	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4802185	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59000923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59827264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61607741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509094	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71362654	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7248167	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap]
rs7248927	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7252962	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7253177	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7253856	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap]
rs762506	0.84[CEU][hapmap]
rs8100211	0.87[EUR][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	esv2762041	chr19:43986023-44014457	Strong transcription Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4802183	ETHE1	Cis_1M	lymphoblastoid	RTeQTL
rs4802183	BLOC1S3	cis	parietal	SCAN
rs4802183	ETHE1	cis	lymphoblastoid	seeQTL
rs4802183	LOC653583///PHLDB3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44007200-44009400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr19:44007400-44009400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr19:44007400-44009400	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr19:44007600-44009400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr19:44007600-44009400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
6	chr19:44007600-44009400	Active TSS	NHDF-Ad	bronchial
7	chr19:44007800-44009400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr19:44007800-44009400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr19:44007800-44009400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
10	chr19:44007800-44009400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:44007800-44009400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr19:44007800-44009400	Active TSS	Brain Cingulate Gyrus	brain
13	chr19:44008200-44009400	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr19:44008400-44009400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr19:44008400-44009600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:44008600-44009400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:44008600-44009400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr19:44008600-44009400	Enhancers	Fetal Brain Male	brain
19	chr19:44008600-44009400	Flanking Active TSS	Fetal Muscle Leg	muscle
20	chr19:44008600-44009400	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr19:44008600-44009400	Flanking Active TSS	Dnd41	blood
22	chr19:44008600-44009400	Flanking Active TSS	HUVEC	blood vessel
23	chr19:44008600-44009400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr19:44008600-44009600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:44008800-44009400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr19:44008800-44009400	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr19:44008800-44009400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr19:44008800-44009400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr19:44008800-44009400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr19:44008800-44009400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr19:44008800-44009400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:44008800-44009400	Flanking Active TSS	Brain Germinal Matrix	brain
33	chr19:44008800-44009400	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr19:44008800-44009400	Flanking Active TSS	Fetal Brain Female	brain
35	chr19:44008800-44009400	Enhancers	Fetal Heart	heart
36	chr19:44008800-44009400	Flanking Active TSS	Thymus	Thymus
37	chr19:44008800-44009600	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr19:44009000-44009400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr19:44009000-44009400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:44009000-44009400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr19:44009000-44009400	Enhancers	Primary B cells from cord blood	blood
42	chr19:44009000-44009400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr19:44009000-44009400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr19:44009000-44009400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr19:44009000-44009400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr19:44009000-44009400	Flanking Active TSS	Brain Anterior Caudate	brain
47	chr19:44009000-44009400	Flanking Active TSS	Brain Hippocampus Middle	brain
48	chr19:44009000-44009400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr19:44009000-44009400	Enhancers	Fetal Lung	lung
50	chr19:44009000-44009400	Enhancers	Placenta	Placenta

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