Variant report

Variant	rs7253533
Chromosome Location	chr19:44711623-44711624
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	POLR2A	chr19:44711291-44712110	GM12878	blood:	n/a	n/a
2	GABPA	chr19:44711366-44711820	H1-hESC	embryonic stem cell:	n/a	chr19:44711642-44711649
3	PAX5	chr19:44711396-44711938	GM12878	blood:	n/a	chr19:44711639-44711648
4	SIN3AK20	chr19:44711346-44711749	A549	lung:	n/a	n/a
5	STAT3	chr19:44711514-44711793	MCF10A-Er-Src	breast:	n/a	chr19:44711701-44711712 chr19:44711601-44711609
6	KAP1	chr19:44711322-44712004	U2OS	brain:	n/a	chr19:44711689-44711697
7	POLR2A	chr19:44711353-44712050	K562	blood:	n/a	n/a
8	YY1	chr19:44711392-44711862	ECC-1	luminal epithelium:	n/a	n/a
9	TBP	chr19:44711206-44712007	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:44711591-44711851	HepG2	liver:	n/a	n/a
11	POLR2A	chr19:44711307-44711980	PANC-1	pancreas:	n/a	n/a
12	ELF1	chr19:44711133-44712069	MCF-7	breast:	n/a	chr19:44711639-44711650 chr19:44711528-44711537 chr19:44711527-44711538 chr19:44711639-44711650 chr19:44711640-44711649
13	GABPA	chr19:44711338-44712005	K562	blood:	n/a	chr19:44711642-44711649
14	JUN	chr19:44710999-44711739	K562	blood:	n/a	n/a
15	POLR2A	chr19:44711392-44711948	GM18951	blood:	n/a	n/a
16	BRCA1	chr19:44711282-44711894	Hela-S3	cervix:	n/a	chr19:44711441-44711448
17	MBD4	chr19:44711365-44711865	HepG2	liver:	n/a	n/a
18	TCF12	chr19:44711209-44712085	A549	lung:	n/a	chr19:44711838-44711845 chr19:44711836-44711846
19	POLR2A	chr19:44711411-44711962	GM15510	blood:	n/a	n/a
20	USF1	chr19:44711345-44711761	A549	lung:	n/a	n/a
21	YY1	chr19:44711340-44712025	SK-N-SH	brain:	n/a	n/a
22	RCOR1	chr19:44711356-44711804	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:44711344-44712035	SK-N-SH	brain:	n/a	n/a
24	MAX	chr19:44711376-44711916	GM12878	blood:	n/a	n/a
25	YY1	chr19:44711399-44711811	H1-hESC	embryonic stem cell:	n/a	n/a
26	YY1	chr19:44711409-44711853	HepG2	liver:	n/a	n/a
27	CEBPB	chr19:44711249-44711782	A549	lung:	n/a	n/a
28	GABPA	chr19:44711393-44711699	Hela-S3	cervix:	n/a	chr19:44711642-44711649
29	E2F6	chr19:44711327-44712042	A549	lung:	n/a	n/a
30	ZNF384	chr19:44711521-44711872	K562	blood:	n/a	n/a
31	ELF1	chr19:44711147-44712139	HCT-116	colon:	n/a	chr19:44711639-44711650 chr19:44711528-44711537 chr19:44711527-44711538 chr19:44711639-44711650 chr19:44711640-44711649
32	SIN3AK20	chr19:44711328-44712130	MCF-7	breast:	n/a	n/a
33	STAT3	chr19:44711188-44711998	MCF10A-Er-Src	breast:	n/a	chr19:44711701-44711712 chr19:44711601-44711609
34	ELK4	chr19:44711400-44711708	HEK293	kidney:	n/a	chr19:44711528-44711539 chr19:44711552-44711563
35	GTF2F1	chr19:44711340-44711907	H1-hESC	embryonic stem cell:	n/a	n/a
36	SIN3AK20	chr19:44711443-44711976	HepG2	liver:	n/a	n/a
37	SIX5	chr19:44711315-44711921	H1-hESC	embryonic stem cell:	n/a	chr19:44711605-44711614 chr19:44711607-44711616
38	POLR2A	chr19:44711272-44711977	HepG2	liver:	n/a	n/a
39	YY1	chr19:44711149-44712157	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr19:44711562-44711827	A549	lung:	n/a	n/a
41	ELF1	chr19:44711327-44712044	GM12878	blood:	n/a	chr19:44711639-44711650 chr19:44711528-44711537 chr19:44711527-44711538 chr19:44711639-44711650 chr19:44711640-44711649
42	PML	chr19:44711514-44711806	GM12878	blood:	n/a	chr19:44711689-44711697
43	STAT1	chr19:44711412-44711985	GM12878	blood:	n/a	chr19:44711601-44711609
44	YY1	chr19:44711289-44711953	A549	lung:	n/a	n/a
45	YY1	chr19:44711417-44711799	K562	blood:	n/a	n/a
46	GABPA	chr19:44710973-44712238	A549	lung:	n/a	chr19:44711642-44711649
47	POLR2A	chr19:44711430-44711989	H1-hESC	embryonic stem cell:	n/a	n/a
48	RFX5	chr19:44711348-44712123	Hela-S3	cervix:	n/a	chr19:44711697-44711712
49	REST	chr19:44711432-44711953	SK-N-SH	brain:	n/a	n/a
50	ELK1	chr19:44711210-44711925	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44711494..44713254-chr19:45003869..45006588,2	MCF-7	breast:
2	chr19:44596073..44597984-chr19:44710588..44712283,2	K562	blood:
3	chr19:44668036..44670553-chr19:44709491..44711796,2	MCF-7	breast:
4	chr19:44709921..44713618-chr19:44714834..44717350,4	K562	blood:
5	chr19:44710790..44713844-chr19:44714955..44718823,7	MCF-7	breast:
6	chr19:44711481..44713542-chr19:44808275..44810056,2	K562	blood:

Variant related genes	Relation type
ZNF227	TF binding region
ENSG00000167384	Chromatin interaction
ENSG00000159917	Chromatin interaction
ENSG00000265842	Chromatin interaction
ENSG00000167380	Chromatin interaction
ENSG00000131115	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10405450	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10410086	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10423306	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10425945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11666199	0.84[EUR][1000 genomes]
rs11667521	0.85[CEU][hapmap]
rs12459795	0.85[EUR][1000 genomes]
rs12460039	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12462557	0.84[CEU][hapmap]
rs12462723	0.85[CEU][hapmap]
rs12608984	0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12972784	0.89[EUR][1000 genomes]
rs12975546	0.85[CEU][hapmap]
rs12980565	0.85[CEU][hapmap]
rs2051059	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs2085516	0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2100643	0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2125579	0.85[CEU][hapmap]
rs2168989	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2232801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279072	0.96[CEU][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2279073	0.85[CEU][hapmap]
rs2293587	0.87[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.87[ASN][1000 genomes]
rs2356751	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.87[ASN][1000 genomes]
rs3817595	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.87[ASN][1000 genomes]
rs4802218	0.84[CEU][hapmap]
rs56357907	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs58778698	0.87[ASN][1000 genomes]
rs60668498	0.81[ASN][1000 genomes]
rs61412562	0.83[ASN][1000 genomes]
rs61589395	0.83[ASN][1000 genomes]
rs62117770	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6509146	0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7248114	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7249209	0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7251682	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7253196	0.86[EUR][1000 genomes]
rs7259916	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7260304	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8101032	0.85[CEU][hapmap]
rs8102037	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8105073	0.87[CEU][hapmap]
rs8108934	0.83[EUR][1000 genomes]
rs9304640	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9646643	0.85[CEU][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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44710400-44713400	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr19:44710600-44711800	Active TSS	Rectal Smooth Muscle	rectum
3	chr19:44710600-44711800	Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr19:44711000-44711800	Active TSS	Monocytes-CD14+_RO01746	blood
5	chr19:44711000-44712000	Active TSS	Fetal Brain Male	brain
6	chr19:44711000-44712400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:44711200-44711800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
8	chr19:44711200-44711800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
9	chr19:44711200-44711800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:44711200-44711800	Active TSS	Duodenum Mucosa	Duodenum
11	chr19:44711200-44712000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:44711200-44712000	Active TSS	Adipose Nuclei	Adipose
13	chr19:44711200-44712000	Active TSS	Brain Cingulate Gyrus	brain
14	chr19:44711200-44712200	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr19:44711200-44712200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
16	chr19:44711200-44712200	Flanking Active TSS	Primary B cells from peripheral blood	blood
17	chr19:44711200-44712200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr19:44711200-44712200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr19:44711200-44712200	Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr19:44711200-44712200	Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr19:44711200-44712200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:44711200-44712200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr19:44711200-44712200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr19:44711200-44712200	Active TSS	Brain Substantia Nigra	brain
25	chr19:44711200-44712200	Active TSS	Fetal Brain Female	brain
26	chr19:44711200-44712200	Active TSS	Fetal Muscle Trunk	muscle
27	chr19:44711200-44712200	Active TSS	Left Ventricle	heart
28	chr19:44711200-44712200	Active TSS	Ovary	ovary
29	chr19:44711200-44712200	Active TSS	Pancreas	Pancrea
30	chr19:44711200-44712200	Active TSS	Right Ventricle	heart
31	chr19:44711200-44712200	Active TSS	Stomach Mucosa	stomach
32	chr19:44711200-44712400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:44711200-44712400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr19:44711200-44712400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr19:44711200-44712400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:44711200-44712400	Active TSS	Brain Angular Gyrus	brain
37	chr19:44711200-44712400	Active TSS	Brain Germinal Matrix	brain
38	chr19:44711200-44712400	Active TSS	Brain Hippocampus Middle	brain
39	chr19:44711200-44712400	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr19:44711200-44712400	Active TSS	Colon Smooth Muscle	Colon
41	chr19:44711200-44712400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr19:44711200-44712400	Active TSS	Fetal Heart	heart
43	chr19:44711200-44712400	Active TSS	Fetal Kidney	kidney
44	chr19:44711200-44712400	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr19:44711200-44712400	Active TSS	Fetal Muscle Leg	muscle
46	chr19:44711200-44712400	Active TSS	Fetal Stomach	stomach
47	chr19:44711200-44712400	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr19:44711200-44712400	Active TSS	Stomach Smooth Muscle	stomach
49	chr19:44711200-44712400	Active TSS	HSMM	muscle
50	chr19:44711200-44712400	Active TSS	NH-A	brain

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