Variant report

Variant	rs11879588
Chromosome Location	chr19:44711211-44711212
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	TBP	chr19:44711206-44712007	GM12878	blood:	n/a	n/a
2	ELF1	chr19:44711133-44712069	MCF-7	breast:	n/a	chr19:44711639-44711650 chr19:44711528-44711537 chr19:44711527-44711538 chr19:44711639-44711650 chr19:44711640-44711649
3	JUN	chr19:44710999-44711739	K562	blood:	n/a	n/a
4	TCF12	chr19:44711209-44712085	A549	lung:	n/a	chr19:44711838-44711845 chr19:44711836-44711846
5	ELF1	chr19:44711147-44712139	HCT-116	colon:	n/a	chr19:44711639-44711650 chr19:44711528-44711537 chr19:44711527-44711538 chr19:44711639-44711650 chr19:44711640-44711649
6	STAT3	chr19:44711188-44711998	MCF10A-Er-Src	breast:	n/a	chr19:44711701-44711712 chr19:44711601-44711609
7	YY1	chr19:44711149-44712157	SK-N-SH	brain:	n/a	n/a
8	GABPA	chr19:44710973-44712238	A549	lung:	n/a	chr19:44711642-44711649
9	ELK1	chr19:44711210-44711925	GM12878	blood:	n/a	n/a
10	ETS1	chr19:44711202-44711933	A549	lung:	n/a	chr19:44711639-44711648 chr19:44711546-44711563 chr19:44711636-44711651 chr19:44711529-44711540 chr19:44711546-44711563 chr19:44711636-44711652 chr19:44711637-44711647 chr19:44711604-44711617 chr19:44711637-44711648
11	POLR2A	chr19:44711148-44712072	SK-N-MC	brain:	n/a	n/a
12	GABPA	chr19:44711076-44712124	SK-N-SH	brain:	n/a	chr19:44711642-44711649
13	ELF1	chr19:44711131-44711976	A549	lung:	n/a	chr19:44711639-44711650 chr19:44711528-44711537 chr19:44711527-44711538 chr19:44711639-44711650 chr19:44711640-44711649
14	GABPA	chr19:44711186-44711982	MCF-7	breast:	n/a	chr19:44711642-44711649
15	GABPA	chr19:44711192-44711932	HL-60	blood:	n/a	chr19:44711642-44711649
16	NFIC	chr19:44711193-44712056	GM12878	blood:	n/a	n/a
17	TBL1XR1	chr19:44711196-44711792	K562	blood:	n/a	n/a
18	REST	chr19:44711198-44712121	H1-neurons	neurons:	n/a	n/a
19	GABPA	chr19:44710946-44712257	MCF-7	breast:	n/a	chr19:44711642-44711649
20	SIX5	chr19:44711178-44711922	A549	lung:	n/a	chr19:44711605-44711614 chr19:44711607-44711616
21	SIX5	chr19:44711093-44712147	A549	lung:	n/a	chr19:44711605-44711614 chr19:44711607-44711616
22	GABPA	chr19:44711050-44711972	HL-60	blood:	n/a	chr19:44711642-44711649
23	ELF1	chr19:44711197-44712042	GM12878	blood:	n/a	chr19:44711639-44711650 chr19:44711528-44711537 chr19:44711527-44711538 chr19:44711639-44711650 chr19:44711640-44711649
24	MAX	chr19:44711177-44712104	A549	lung:	n/a	n/a
25	SPI1	chr19:44711172-44712034	GM12878	blood:	n/a	chr19:44711640-44711649 chr19:44711638-44711651 chr19:44711639-44711652
26	POLR2A	chr19:44711190-44712023	PFSK-1	brain:	n/a	n/a
27	HCFC1	chr19:44710867-44712310	Hela-S3	cervix:	n/a	n/a
28	GABPA	chr19:44711171-44712156	SK-N-SH	brain:	n/a	chr19:44711642-44711649
29	GATA3	chr19:44711120-44712187	A549	lung:	n/a	n/a
30	ELF1	chr19:44711189-44712105	A549	lung:	n/a	chr19:44711639-44711650 chr19:44711528-44711537 chr19:44711527-44711538 chr19:44711639-44711650 chr19:44711640-44711649
31	ETS1	chr19:44711077-44712037	A549	lung:	n/a	chr19:44711639-44711648 chr19:44711546-44711563 chr19:44711636-44711651 chr19:44711529-44711540 chr19:44711546-44711563 chr19:44711636-44711652 chr19:44711637-44711647 chr19:44711604-44711617 chr19:44711637-44711648
32	GABPA	chr19:44711103-44712133	A549	lung:	n/a	chr19:44711642-44711649
33	ELF1	chr19:44711113-44712051	HCT-116	colon:	n/a	chr19:44711639-44711650 chr19:44711528-44711537 chr19:44711527-44711538 chr19:44711639-44711650 chr19:44711640-44711649
34	POLR2A	chr19:44711195-44712100	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr19:44711121-44712248	PFSK-1	brain:	n/a	n/a
36	ELF1	chr19:44711156-44712038	SK-N-SH	brain:	n/a	chr19:44711639-44711650 chr19:44711528-44711537 chr19:44711527-44711538 chr19:44711639-44711650 chr19:44711640-44711649
37	PML	chr19:44711178-44712073	GM12878	blood:	n/a	chr19:44711689-44711697

No.	Distal block	Cell Line	Cell type
1	chr19:44596073..44597984-chr19:44710588..44712283,2	K562	blood:
2	chr19:44668036..44670553-chr19:44709491..44711796,2	MCF-7	breast:
3	chr19:44709921..44713618-chr19:44714834..44717350,4	K562	blood:
4	chr19:44710790..44713844-chr19:44714955..44718823,7	MCF-7	breast:

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

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10153465	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10153499	0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10405281	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10406980	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10408004	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10409884	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10409954	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10410283	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10412910	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10415563	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10415664	0.82[ASN][1000 genomes]
rs10416230	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10416292	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10417178	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10420465	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10422555	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10422609	0.94[ASN][1000 genomes]
rs10424371	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10425146	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10425881	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10426314	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1106562	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11140	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11878679	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11878720	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11879843	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16959114	0.84[ASN][1000 genomes]
rs16978738	0.84[ASN][1000 genomes]
rs16978794	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16978836	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1881748	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2141524	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2141525	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2178342	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28422007	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3803932	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3810137	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4802212	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802213	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802215	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4803683	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4803685	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4803686	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4803688	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4803692	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4803693	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55732275	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57418162	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57451052	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58358390	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59576456	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59774711	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60379253	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60747128	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6509144	0.84[ASN][1000 genomes]
rs6509147	0.94[ASN][1000 genomes]
rs6509148	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7248797	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7249992	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7254034	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7254458	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7260367	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73564059	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73564095	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8107252	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8108504	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8108908	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8111388	0.84[ASN][1000 genomes]
rs922063	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs922064	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9304639	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

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:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44709200-44711600	ZNF genes & repeats	Liver	Liver
2	chr19:44710400-44713400	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr19:44710600-44711800	Active TSS	Rectal Smooth Muscle	rectum
4	chr19:44710600-44711800	Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr19:44711000-44711400	ZNF genes & repeats	Fetal Intestine Large	intestine
6	chr19:44711000-44711400	ZNF genes & repeats	GM12878-XiMat	blood
7	chr19:44711000-44711600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
8	chr19:44711000-44711800	Active TSS	Monocytes-CD14+_RO01746	blood
9	chr19:44711000-44712000	Active TSS	Fetal Brain Male	brain
10	chr19:44711000-44712400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:44711200-44711400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr19:44711200-44711400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
13	chr19:44711200-44711400	Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr19:44711200-44711400	Active TSS	Primary T cells from cord blood	blood
15	chr19:44711200-44711400	Active TSS	Primary T cells fromperipheralblood	blood
16	chr19:44711200-44711400	Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr19:44711200-44711400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr19:44711200-44711400	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:44711200-44711400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
20	chr19:44711200-44711400	Active TSS	Thymus	Thymus
21	chr19:44711200-44711400	ZNF genes & repeats	A549	lung
22	chr19:44711200-44711400	Flanking Active TSS	Hela-S3	cervix
23	chr19:44711200-44711600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:44711200-44711600	Active TSS	Primary B cells from cord blood	blood
25	chr19:44711200-44711600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr19:44711200-44711600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr19:44711200-44711600	Flanking Active TSS	Dnd41	blood
28	chr19:44711200-44711600	Active TSS	HepG2	liver
29	chr19:44711200-44711600	Flanking Active TSS	HUVEC	blood vessel
30	chr19:44711200-44711800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr19:44711200-44711800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr19:44711200-44711800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr19:44711200-44711800	Active TSS	Duodenum Mucosa	Duodenum
34	chr19:44711200-44712000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr19:44711200-44712000	Active TSS	Adipose Nuclei	Adipose
36	chr19:44711200-44712000	Active TSS	Brain Cingulate Gyrus	brain
37	chr19:44711200-44712200	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr19:44711200-44712200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr19:44711200-44712200	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr19:44711200-44712200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr19:44711200-44712200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr19:44711200-44712200	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr19:44711200-44712200	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr19:44711200-44712200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr19:44711200-44712200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr19:44711200-44712200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:44711200-44712200	Active TSS	Brain Substantia Nigra	brain
48	chr19:44711200-44712200	Active TSS	Fetal Brain Female	brain
49	chr19:44711200-44712200	Active TSS	Fetal Muscle Trunk	muscle
50	chr19:44711200-44712200	Active TSS	Left Ventricle	heart

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