Variant report

Variant	rs4459653
Chromosome Location	chr19:44599615-44599616
allele	C/T
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	RAD21	chr19:44599349-44599633	Hela-S3	cervix:	n/a	n/a
2	SREBP1	chr19:44597634-44599876	GM12878	blood:	n/a	chr19:44599340-44599351
3	CTCF	chr19:44599387-44599636	Spleen_OC	spleen:	n/a	n/a
4	IRF1	chr19:44599289-44599699	K562	blood:	n/a	chr19:44599495-44599516
5	POLR2A	chr19:44599579-44599665	ProgFib	skin:	n/a	n/a
6	SMC3	chr19:44599312-44599667	GM12878	blood:	n/a	n/a
7	UBTF	chr19:44598931-44599655	K562	blood:	n/a	n/a
8	SMC3	chr19:44599216-44599624	Hela-S3	cervix:	n/a	n/a
9	USF2	chr19:44599475-44599645	Hela-S3	cervix:	n/a	n/a
10	SIN3AK20	chr19:44598043-44599742	MCF-7	breast:	n/a	n/a
11	ZNF143	chr19:44599375-44599629	GM12878	blood:	n/a	n/a
12	IRF1	chr19:44599317-44599668	K562	blood:	n/a	chr19:44599495-44599516
13	MXI1	chr19:44599331-44599720	GM12878	blood:	n/a	n/a
14	WRNIP1	chr19:44599469-44599667	GM12878	blood:	n/a	n/a
15	PRDM1	chr19:44599296-44599654	Hela-S3	cervix:	n/a	chr19:44599493-44599508
16	FOXM1	chr19:44599278-44599725	GM12878	blood:	n/a	n/a
17	IRF1	chr19:44599397-44599663	K562	blood:	n/a	chr19:44599495-44599516
18	RAD21	chr19:44599042-44599655	IMR90	lung:	n/a	chr19:44599064-44599078
19	CTCF	chr19:44599194-44599647	GM12878	blood:	n/a	n/a
20	BHLHE40	chr19:44599436-44599636	K562	blood:	n/a	n/a
21	BHLHE40	chr19:44599246-44599691	GM12878	blood:	n/a	n/a
22	MYC	chr19:44599390-44599634	K562	blood:	n/a	n/a
23	HCFC1	chr19:44597600-44599794	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44596713..44600957-chr19:44644435..44647275,5	MCF-7	breast:
2	chr19:44555396..44557599-chr19:44598429..44600981,2	MCF-7	breast:
3	chr19:44555737..44557669-chr19:44596681..44600019,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF45-4	chr19:44598503-44599794	ENSG00000267163.1
2	lnc-ZNF284-1	chr19:44598543-44600094	NONHSAT066660

Variant related genes	Relation type
ZNF224	TF binding region
ENSG00000178386	Chromatin interaction
ENSG00000263002	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10406335	0.83[CHB][hapmap]
rs10408901	0.83[CHB][hapmap]
rs10410306	0.83[CHB][hapmap]
rs1236715	0.83[CHB][hapmap];0.88[TSI][hapmap]
rs1236716	0.83[CHB][hapmap];0.83[GIH][hapmap];0.88[TSI][hapmap]
rs2061332	0.91[CHB][hapmap];0.88[GIH][hapmap];0.96[TSI][hapmap]
rs2061333	0.91[CHB][hapmap];0.88[GIH][hapmap];0.96[TSI][hapmap]
rs2068061	0.87[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2284978	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2284980	0.83[CHB][hapmap]
rs2284981	0.83[CHB][hapmap]
rs3172	0.81[CEU][hapmap];0.85[CHB][hapmap];0.86[EUR][1000 genomes]
rs3746319	0.91[CHB][hapmap];0.88[GIH][hapmap];0.96[TSI][hapmap]
rs4239529	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4429390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4508518	0.87[CHB][hapmap];0.91[GIH][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs4802204	0.87[EUR][1000 genomes]
rs4802205	0.85[EUR][1000 genomes]
rs4802206	0.82[CHB][hapmap]
rs4802207	0.83[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs4803676	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4803677	0.98[ASN][1000 genomes]
rs4803678	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4803679	0.98[ASN][1000 genomes]
rs4803680	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4803681	0.83[CEU][hapmap];0.82[CHB][hapmap];0.86[EUR][1000 genomes]
rs56353321	0.86[EUR][1000 genomes]
rs62115524	0.86[EUR][1000 genomes]
rs62115526	0.87[EUR][1000 genomes]
rs6509141	0.93[ASN][1000 genomes]
rs7249827	0.98[ASN][1000 genomes]
rs7249834	0.98[ASN][1000 genomes]
rs7250076	0.97[ASN][1000 genomes]
rs7250171	0.97[ASN][1000 genomes]
rs7508149	0.86[CHB][hapmap]
rs8099869	0.83[CHB][hapmap]
rs8101657	0.98[ASN][1000 genomes]
rs8104573	0.83[CHB][hapmap]
rs8105860	0.83[CHB][hapmap]
rs8108021	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs8113249	0.91[EUR][1000 genomes]
rs9304638	0.83[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4459653	NAPSB	cis	parietal	SCAN
rs4459653	KLK10	cis	cerebellum	SCAN
rs4459653	RRAS	cis	cerebellum	SCAN
rs4459653	MED25	cis	parietal	SCAN
rs4459653	SNORD34	cis	parietal	SCAN
rs4459653	ZNF223	cis	Thyroid	GTEx
rs4459653	SIGLEC12	cis	parietal	SCAN
rs4459653	APOE	cis	parietal	SCAN
rs4459653	CPT1C	cis	cerebellum	SCAN
rs4459653	TULP2	cis	cerebellum	SCAN
rs4459653	FPR2	cis	parietal	SCAN
rs4459653	ZNF224	Cis_1M	lymphoblastoid	RTeQTL
rs4459653	FUT2	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44597800-44599800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:44597800-44599800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:44597800-44599800	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr19:44597800-44599800	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr19:44597800-44599800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr19:44597800-44599800	Active TSS	Primary hematopoietic stem cells	blood
7	chr19:44597800-44599800	Active TSS	Brain Anterior Caudate	brain
8	chr19:44597800-44599800	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr19:44597800-44599800	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr19:44597800-44599800	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr19:44597800-44599800	Active TSS	HMEC	breast
12	chr19:44597800-44599800	Active TSS	K562	blood
13	chr19:44597800-44600000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:44597800-44600000	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr19:44597800-44600000	Active TSS	Primary T cells from cord blood	blood
16	chr19:44597800-44600000	Active TSS	Stomach Smooth Muscle	stomach
17	chr19:44597800-44600000	Active TSS	A549	lung
18	chr19:44597800-44600200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:44598000-44599800	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr19:44598000-44599800	Active TSS	H1 Cell Line	embryonic stem cell
21	chr19:44598000-44599800	Active TSS	H9 Cell Line	embryonic stem cell
22	chr19:44598000-44599800	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr19:44598000-44599800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:44598000-44599800	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr19:44598000-44599800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr19:44598000-44599800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr19:44598000-44599800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr19:44598000-44599800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:44598000-44599800	Active TSS	Brain Angular Gyrus	brain
30	chr19:44598000-44599800	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr19:44598000-44599800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr19:44598000-44599800	Active TSS	Brain Substantia Nigra	brain
33	chr19:44598000-44599800	Active TSS	Colonic Mucosa	Colon
34	chr19:44598000-44599800	Active TSS	Colon Smooth Muscle	Colon
35	chr19:44598000-44599800	Active TSS	Fetal Lung	lung
36	chr19:44598000-44599800	Active TSS	Fetal Muscle Trunk	muscle
37	chr19:44598000-44599800	Active TSS	Placenta	Placenta
38	chr19:44598000-44599800	Active TSS	Left Ventricle	heart
39	chr19:44598000-44599800	Active TSS	Psoas Muscle	Psoas
40	chr19:44598000-44599800	Active TSS	Right Atrium	heart
41	chr19:44598000-44599800	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr19:44598000-44599800	Active TSS	HSMM	muscle
43	chr19:44598000-44599800	Active TSS	HSMMtube	muscle
44	chr19:44598000-44599800	Active TSS	NHDF-Ad	bronchial
45	chr19:44598000-44600000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr19:44598000-44600000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr19:44598000-44600000	Active TSS	Fetal Intestine Large	intestine
48	chr19:44598000-44600000	Active TSS	NHLF	lung
49	chr19:44598000-44600200	Active TSS	Right Ventricle	heart
50	chr19:44598000-44600200	Active TSS	Hela-S3	cervix

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