Variant report

Variant	rs4806641
Chromosome Location	chr19:55592070-55592071
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	YY1	chr19:55592030-55592341	K562	blood:	n/a	n/a
2	MYC	chr19:55591415-55593059	K562	blood:	n/a	chr19:55592036-55592051 chr19:55592038-55592048 chr19:55592038-55592047 chr19:55592542-55592552 chr19:55592039-55592046 chr19:55591937-55591946
3	POLR2A	chr19:55591405-55593048	K562	blood:	n/a	n/a
4	TAL1	chr19:55591465-55592147	K562	blood:	n/a	n/a
5	MYC	chr19:55591152-55592247	A549	lung:	n/a	chr19:55591230-55591237 chr19:55592036-55592051 chr19:55592038-55592048 chr19:55592038-55592047 chr19:55592039-55592046 chr19:55591937-55591946
6	MAX	chr19:55591479-55592177	Hela-S3	cervix:	n/a	chr19:55592036-55592051 chr19:55592038-55592048 chr19:55592038-55592047 chr19:55592039-55592046 chr19:55591937-55591946
7	POLR2A	chr19:55591300-55592301	ECC-1	luminal epithelium:	n/a	n/a
8	MAX	chr19:55591477-55593243	NB4	blood:	n/a	chr19:55592036-55592051 chr19:55592038-55592048 chr19:55592038-55592047 chr19:55592542-55592552 chr19:55592039-55592046 chr19:55591937-55591946
9	BHLHE40	chr19:55591424-55592472	K562	blood:	n/a	n/a
10	POLR2A	chr19:55591405-55593010	K562	blood:	n/a	n/a
11	SPI1	chr19:55591954-55592164	GM12891	blood:	n/a	n/a
12	POLR2A	chr19:55591474-55592193	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr19:55591421-55592969	K562	blood:	n/a	n/a
14	POLR2A	chr19:55591376-55593019	K562	blood:	n/a	n/a
15	POLR2A	chr19:55591013-55593186	MCF-7	breast:	n/a	n/a
16	POLR2A	chr19:55591612-55592112	MCF10A-Er-Src	breast:	n/a	n/a
17	E2F6	chr19:55591108-55592958	K562	blood:	n/a	n/a
18	POLR2A	chr19:55591215-55594182	H1-hESC	embryonic stem cell:	n/a	n/a
19	PBX3	chr19:55592016-55592218	GM12878	blood:	n/a	chr19:55592130-55592139
20	POLR2A	chr19:55591373-55592403	HL-60	blood:	n/a	n/a
21	POLR2A	chr19:55591329-55592998	K562	blood:	n/a	n/a
22	POLR2A	chr19:55591891-55592145	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:55590829-55593392	K562	blood:	n/a	n/a
24	CTCF	chr19:55592014-55592226	K562	blood:	n/a	n/a
25	MYC	chr19:55591954-55592107	HUVEC	blood vessel:	n/a	chr19:55592036-55592051 chr19:55592038-55592048 chr19:55592038-55592047 chr19:55592039-55592046
26	TCF3	chr19:55591784-55592127	GM12878	blood:	n/a	chr19:55592016-55592032 chr19:55592016-55592031 chr19:55591965-55591978
27	POLR2A	chr19:55591401-55593019	NB4	blood:	n/a	n/a
28	RCOR1	chr19:55590779-55592847	K562	blood:	n/a	n/a
29	MAX	chr19:55591863-55592223	HepG2	liver:	n/a	chr19:55592036-55592051 chr19:55592038-55592048 chr19:55592038-55592047 chr19:55592039-55592046 chr19:55591937-55591946
30	CTCF	chr19:55591943-55592844	K562	blood:	n/a	n/a
31	PAX5	chr19:55591851-55592196	GM12878	blood:	n/a	n/a
32	E2F6	chr19:55591398-55592302	K562	blood:	n/a	n/a
33	MYC	chr19:55591777-55592252	MCF-7	breast:	n/a	chr19:55592036-55592051 chr19:55592038-55592048 chr19:55592038-55592047 chr19:55592039-55592046 chr19:55591937-55591946
34	ZMIZ1	chr19:55591530-55592319	K562	blood:	n/a	n/a
35	POLR2A	chr19:55591739-55592433	H1-hESC	embryonic stem cell:	n/a	n/a
36	TBL1XR1	chr19:55591635-55592123	K562	blood:	n/a	n/a
37	SPI1	chr19:55591971-55592207	K562	blood:	n/a	n/a
38	EGR1	chr19:55591528-55592235	K562	blood:	n/a	chr19:55591910-55591920
39	MYC	chr19:55591409-55592441	K562	blood:	n/a	chr19:55592036-55592051 chr19:55592038-55592048 chr19:55592038-55592047 chr19:55592039-55592046 chr19:55591937-55591946
40	EGR1	chr19:55591524-55592231	K562	blood:	n/a	chr19:55591910-55591920
41	CTCF	chr19:55592037-55592315	K562	blood:	n/a	n/a
42	MYC	chr19:55591844-55592180	MCF-7	breast:	n/a	chr19:55592036-55592051 chr19:55592038-55592048 chr19:55592038-55592047 chr19:55592039-55592046 chr19:55591937-55591946
43	CBX3	chr19:55590613-55593218	K562	blood:	n/a	n/a
44	POLR2A	chr19:55591995-55592192	HUVEC	blood vessel:	n/a	n/a
45	PAX5	chr19:55592033-55592287	GM12892	blood:	n/a	n/a
46	POLR2A	chr19:55591331-55592134	U87	brain:	n/a	n/a
47	PBX3	chr19:55591788-55592384	A549	lung:	n/a	chr19:55592130-55592139
48	POLR2A	chr19:55591671-55592133	Hela-S3	cervix:	n/a	n/a
49	MAX	chr19:55591379-55592361	A549	lung:	n/a	chr19:55592036-55592051 chr19:55592038-55592048 chr19:55592038-55592047 chr19:55592039-55592046 chr19:55591937-55591946
50	MXI1	chr19:55591587-55592174	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:55590282..55593983-chr19:55668450..55672239,5	K562	blood:
2	chr19:55591269..55595027-chr19:55600800..55604307,4	MCF-7	breast:
3	chr19:55579877..55582697-chr19:55590246..55594605,5	K562	blood:
4	chr19:55590451..55592160-chr19:56109992..56112858,2	K562	blood:
5	chr19:55590321..55593325-chr19:55662374..55666146,3	K562	blood:
6	chr19:55584232..55587970-chr19:55588941..55594707,6	MCF-7	breast:
7	chr19:55591309..55594573-chr19:55626629..55629730,4	MCF-7	breast:
8	chr19:55583728..55588603-chr19:55588891..55593103,7	K562	blood:
9	chr19:55537400..55539426-chr19:55591355..55593225,2	K562	blood:
10	chr19:55543467..55545505-chr19:55591286..55592893,2	K562	blood:
11	chr19:55590301..55596157-chr19:55624719..55630906,19	K562	blood:
12	chr19:55590426..55594638-chr19:55684228..55687886,4	K562	blood:
13	chr19:55547122..55550038-chr19:55591373..55593222,2	K562	blood:
14	chr19:55579423..55583045-chr19:55590822..55594166,5	MCF-7	breast:
15	chr19:55574779..55578954-chr19:55590398..55594780,7	K562	blood:
16	chr19:55590620..55592858-chr19:55916927..55919392,2	K562	blood:
17	chr19:55590507..55594768-chr19:55917232..55920967,4	K562	blood:
18	chr19:54974707..54977217-chr19:55590238..55592841,2	K562	blood:
19	chr19:54972603..54977373-chr19:55591252..55593006,5	MCF-7	breast:
20	chr19:55591561..55594163-chr19:55604044..55608526,4	K562	blood:
21	chr19:55591466..55594430-chr19:55604044..55607280,3	K562	blood:
22	chr19:55591753..55593275-chr19:55598361..55600388,2	MCF-7	breast:
23	chr19:55591162..55592907-chr19:56164329..56166791,2	K562	blood:
24	chr19:55585770..55588599-chr19:55589923..55593327,7	K562	blood:
25	chr19:55585799..55587741-chr19:55590288..55592473,2	MCF-7	breast:
26	chr19:55591142..55593634-chr19:55888302..55890512,2	K562	blood:
27	chr19:55589341..55594280-chr19:55623400..55630615,14	K562	blood:
28	chr19:55591899..55594661-chr19:55659988..55661544,2	K562	blood:
29	chr19:55574558..55577984-chr19:55590398..55594592,5	K562	blood:
30	chr19:55589568..55594642-chr19:55594653..55598392,9	MCF-7	breast:
31	chr19:55592011..55594638-chr19:55684282..55687431,3	K562	blood:
32	chr19:55590129..55594149-chr19:55677127..55678963,3	K562	blood:

Variant related genes	Relation type
EPS8L1	TF binding region
ENSG00000182909	Chromatin interaction
ENSG00000125503	Chromatin interaction
ENSG00000105048	Chromatin interaction
ENSG00000269275	Chromatin interaction
ENSG00000129991	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000267577	Chromatin interaction
ENSG00000160439	Chromatin interaction
ENSG00000239137	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000131037	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000267265	Chromatin interaction
ENSG00000167646	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000088053	Chromatin interaction
ENSG00000267110	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1860325	1.00[ASW][hapmap];0.84[CEU][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs2603700	0.89[EUR][1000 genomes]
rs575144	0.84[TSI][hapmap]
rs667451	0.84[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3319164	chr19:54983548-55605784	Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	esv3319165	chr19:54983548-55605784	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	esv3395724	chr19:54983577-55605784	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats 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	79 gene(s)	inside rSNPs	diseases
4	esv3341592	chr19:54983611-55605750	Weak transcription Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
5	nsv534462	chr19:55028722-55683018	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
6	nsv1063666	chr19:55030439-55622780	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4806641	RDH13	cis	Artery Tibial	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55590400-55592200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
2	chr19:55590400-55592800	Enhancers	Placenta Amnion	Placenta Amnion
3	chr19:55590800-55594000	Genic enhancers	Gastric	stomach
4	chr19:55591000-55592200	Bivalent Enhancer	Spleen	Spleen
5	chr19:55591000-55592600	Transcr. at gene 5' and 3'	Esophagus	oesophagus
6	chr19:55591000-55593400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr19:55591000-55594000	Active TSS	H9 Cell Line	embryonic stem cell
8	chr19:55591200-55592200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
9	chr19:55591200-55592400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:55591200-55593000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:55591200-55594000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr19:55591400-55592200	Enhancers	HUVEC	blood vessel
13	chr19:55591400-55592400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:55591400-55592400	Bivalent/Poised TSS	Psoas Muscle	Psoas
15	chr19:55591400-55592600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr19:55591400-55592800	Enhancers	Stomach Mucosa	stomach
17	chr19:55591400-55593200	Bivalent Enhancer	Fetal Heart	heart
18	chr19:55591400-55593600	Bivalent/Poised TSS	HSMM	muscle
19	chr19:55591400-55594000	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr19:55591400-55594200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
21	chr19:55591400-55594600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
22	chr19:55591600-55592400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr19:55591600-55593000	Flanking Bivalent TSS/Enh	Thymus	Thymus
24	chr19:55591600-55593200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr19:55591600-55593400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr19:55591800-55592200	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr19:55591800-55592200	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:55591800-55592200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr19:55591800-55592200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:55591800-55592200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:55591800-55592200	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr19:55591800-55592200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
33	chr19:55591800-55592200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
34	chr19:55591800-55592200	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr19:55591800-55592200	Bivalent/Poised TSS	Fetal Kidney	kidney
36	chr19:55591800-55592200	Flanking Bivalent TSS/Enh	Left Ventricle	heart
37	chr19:55591800-55592200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
38	chr19:55591800-55592200	Bivalent/Poised TSS	Osteobl	bone
39	chr19:55591800-55592400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:55591800-55592400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:55591800-55592400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr19:55591800-55592400	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
43	chr19:55591800-55592400	Flanking Bivalent TSS/Enh	HepG2	liver
44	chr19:55591800-55592600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr19:55591800-55592600	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
46	chr19:55591800-55592600	Flanking Active TSS	Hela-S3	cervix
47	chr19:55591800-55592600	Flanking Active TSS	NHEK	skin
48	chr19:55591800-55592800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr19:55591800-55592800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
50	chr19:55591800-55592800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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