Variant report

Variant	rs3761087
Chromosome Location	chr19:36235431-36235432
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	USF1	chr19:36235272-36235883	A549	lung:	n/a	n/a
2	POLR2A	chr19:36235346-36236702	GM12878	blood:	n/a	n/a
3	EP300	chr19:36235396-36236473	A549	lung:	n/a	n/a
4	MAX	chr19:36235184-36237068	A549	lung:	n/a	chr19:36235447-36235457 chr19:36236419-36236435
5	POLR2A	chr19:36234509-36236730	GM12878	blood:	n/a	n/a
6	MXI1	chr19:36235293-36237237	IMR90	lung:	n/a	n/a
7	POLR2A	chr19:36234795-36235646	K562	blood:	n/a	n/a
8	EGR1	chr19:36235255-36235620	K562	blood:	n/a	chr19:36235444-36235457 chr19:36235447-36235457
9	POLR2A	chr19:36235407-36236899	PANC-1	pancreas:	n/a	n/a
10	PBX3	chr19:36235305-36235573	GM12878	blood:	n/a	n/a
11	SP1	chr19:36235305-36236936	A549	lung:	n/a	chr19:36235611-36235620 chr19:36235626-36235640 chr19:36235610-36235619 chr19:36235667-36235681 chr19:36235609-36235621 chr19:36236173-36236182 chr19:36235610-36235620 chr19:36235449-36235458 chr19:36236735-36236744 chr19:36236734-36236744 chr19:36235611-36235620 chr19:36235608-36235615 chr19:36235610-36235620 chr19:36235609-36235621 chr19:36236671-36236680 chr19:36236734-36236744
12	POLR2A	chr19:36235399-36236759	GM12878	blood:	n/a	n/a
13	MAX	chr19:36235414-36236728	MCF-7	breast:	n/a	chr19:36235447-36235457 chr19:36236419-36236435
14	POLR2A	chr19:36235376-36236726	GM18505	blood:	n/a	n/a
15	MAX	chr19:36235382-36236842	A549	lung:	n/a	chr19:36235447-36235457 chr19:36236419-36236435
16	MAZ	chr19:36235328-36237351	IMR90	lung:	n/a	chr19:36235447-36235457 chr19:36236419-36236435
17	SIN3AK20	chr19:36235345-36236906	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr19:36235416-36236728	GM12892	blood:	n/a	n/a
19	CREB1	chr19:36235333-36236666	K562	blood:	n/a	n/a
20	MAZ	chr19:36235393-36236745	GM12878	blood:	n/a	chr19:36235447-36235457 chr19:36236419-36236435
21	POLR2A	chr19:36235342-36236757	GM19193	blood:	n/a	n/a
22	BCL3	chr19:36235161-36237015	A549	lung:	n/a	chr19:36236330-36236339
23	POLR2A	chr19:36235074-36236854	H1-hESC	embryonic stem cell:	n/a	n/a
24	BHLHE40	chr19:36235354-36236511	GM12878	blood:	n/a	n/a
25	BCL3	chr19:36235409-36236984	A549	lung:	n/a	chr19:36236330-36236339
26	CHD1	chr19:36235309-36237067	IMR90	lung:	n/a	chr19:36235450-36235460
27	USF1	chr19:36235201-36235514	K562	blood:	n/a	n/a
28	POLR2A	chr19:36234647-36236740	GM12878	blood:	n/a	n/a
29	CREB1	chr19:36235273-36236825	HepG2	liver:	n/a	n/a
30	SIN3AK20	chr19:36235310-36236956	MCF-7	breast:	n/a	n/a
31	PML	chr19:36235209-36236824	GM12878	blood:	n/a	n/a
32	SP1	chr19:36235227-36236757	A549	lung:	n/a	chr19:36235611-36235620 chr19:36235626-36235640 chr19:36235610-36235619 chr19:36235667-36235681 chr19:36235609-36235621 chr19:36236173-36236182 chr19:36235610-36235620 chr19:36235449-36235458 chr19:36236735-36236744 chr19:36236734-36236744 chr19:36235611-36235620 chr19:36235608-36235615 chr19:36235610-36235620 chr19:36235609-36235621 chr19:36236671-36236680 chr19:36236734-36236744
33	USF1	chr19:36235275-36235622	K562	blood:	n/a	n/a
34	CREB1	chr19:36235218-36236867	GM12878	blood:	n/a	n/a
35	SP1	chr19:36235427-36236657	GM12878	blood:	n/a	chr19:36235611-36235620 chr19:36235626-36235640 chr19:36235610-36235619 chr19:36235667-36235681 chr19:36235609-36235621 chr19:36236173-36236182 chr19:36235610-36235620 chr19:36235449-36235458 chr19:36235611-36235620 chr19:36235608-36235615 chr19:36235610-36235620 chr19:36235609-36235621
36	HCFC1	chr19:36235387-36237068	Hela-S3	cervix:	n/a	n/a
37	ELF1	chr19:36235394-36236689	GM12878	blood:	n/a	n/a
38	BHLHE40	chr19:36235382-36236474	K562	blood:	n/a	n/a
39	MAFK	chr19:36235387-36235436	K562	blood:	n/a	n/a
40	JUN	chr19:36235339-36236843	K562	blood:	n/a	chr19:36236599-36236607
41	POU2F2	chr19:36235281-36236785	GM12878	blood:	n/a	chr19:36236176-36236188
42	SIX5	chr19:36235266-36237101	A549	lung:	n/a	chr19:36236353-36236362 chr19:36236355-36236364 chr19:36236352-36236366 chr19:36236506-36236520
43	POLR2A	chr19:36235211-36236801	Raji	blood:	n/a	n/a
44	EGR1	chr19:36235306-36235552	K562	blood:	n/a	chr19:36235444-36235457 chr19:36235447-36235457
45	CTCF	chr19:36235420-36235570	SK-N-SH_RA	brain:	n/a	n/a
46	CREB1	chr19:36235234-36236821	GM12878	blood:	n/a	n/a
47	POLR2A	chr19:36235308-36236732	GM12892	blood:	n/a	n/a
48	CBX3	chr19:36235245-36236140	K562	blood:	n/a	n/a
49	POLR2A	chr19:36235400-36236739	GM18951	blood:	n/a	n/a
50	GABPA	chr19:36235404-36236859	SK-N-SH	brain:	n/a	chr19:36235453-36235462 chr19:36236473-36236482 chr19:36236473-36236484 chr19:36236411-36236422 chr19:36236470-36236484 chr19:36236413-36236422

No.	Distal block	Cell Line	Cell type
1	chr19:36207379..36214815-chr19:36234227..36241330,25	MCF-7	breast:
2	chr19:36223134..36225733-chr19:36234939..36237543,2	MCF-7	breast:
3	chr19:36035683..36038067-chr19:36234353..36237102,3	K562	blood:
4	chr19:36234776..36236564-chr19:36265019..36266986,2	K562	blood:
5	chr19:36234932..36236574-chr19:36258515..36260489,2	K562	blood:
6	chr19:36234786..36236387-chr19:36265803..36268215,2	MCF-7	breast:
7	chr19:35643125..35645834-chr19:36235394..36237704,2	K562	blood:
8	chr19:36034766..36037168-chr19:36234979..36237516,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-U2AF1L4-1	chr19:36234971-36236113	NONHSAT065900
2	lnc-U2AF1L4-1	chr19:36234971-36236113	NONHSAT065902

Variant related genes	Relation type
LIN37	TF binding region
IGFLR1	TF binding region
ENSG00000188223	TF binding region
PSENEN	TF binding region
ENSG00000089327	Chromatin interaction
ENSG00000105677	Chromatin interaction
ENSG00000004777	Chromatin interaction
ENSG00000105663	Chromatin interaction
ENSG00000236144	Chromatin interaction
ENSG00000167595	Chromatin interaction
ENSG00000272333	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10401156	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10402601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10402837	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11549030	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459634	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2239947	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28656784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871921	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34031911	0.82[AFR][1000 genomes]
rs3746277	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3848662	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3848665	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62112162	0.87[EUR][1000 genomes]
rs7260184	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
3	nsv458566	chr19:36156588-36265508	Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv579422	chr19:36156588-36265508	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv911631	chr19:36169285-36290977	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv911632	chr19:36174176-36288297	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv911633	chr19:36206050-36283847	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
8	nsv911634	chr19:36206050-36290977	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
9	nsv543996	chr19:36210269-36265431	Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv1057830	chr19:36210269-36279794	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv543997	chr19:36210269-36279794	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
12	nsv911635	chr19:36217333-36283847	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv515536	chr19:36219525-36240960	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
14	nsv458567	chr19:36221051-36283847	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
15	nsv579423	chr19:36221051-36283847	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3761087	U2AF1L4	cis	Whole Blood	GTEx
rs3761087	TMEM149	Cis_1M	lymphoblastoid	RTeQTL
rs3761087	U2AF1L4	cis	lung	GTEx
rs3761087	U2AF1L4	Cis_1M	lymphoblastoid	RTeQTL
rs3761087	U2AF1L4	cis	Esophagus Muscularis	GTEx
rs3761087	U2AF1L4	cis	Muscle Skeletal	GTEx
rs3761087	TMEM149	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36234600-36235600	Flanking Active TSS	Primary T cells from cord blood	blood
2	chr19:36234600-36235600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
3	chr19:36234600-36235600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr19:36234600-36235600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
5	chr19:36234600-36235800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr19:36234800-36235600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
7	chr19:36234800-36235600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
8	chr19:36234800-36235600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
9	chr19:36234800-36235800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
10	chr19:36234800-36235800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
11	chr19:36234800-36235800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr19:36234800-36235800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr19:36234800-36235800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr19:36234800-36236200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
15	chr19:36235000-36235600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr19:36235000-36235600	Enhancers	Fetal Brain Male	brain
17	chr19:36235000-36235600	Flanking Active TSS	GM12878-XiMat	blood
18	chr19:36235000-36235800	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr19:36235000-36235800	Flanking Active TSS	Primary B cells from peripheral blood	blood
20	chr19:36235000-36235800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:36235000-36235800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:36235000-36235800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:36235000-36235800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr19:36235000-36235800	Flanking Active TSS	Brain Germinal Matrix	brain
25	chr19:36235000-36236000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr19:36235000-36237200	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr19:36235000-36237800	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr19:36235200-36235600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
29	chr19:36235200-36235600	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:36235200-36235600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr19:36235200-36235600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr19:36235200-36235600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:36235200-36235600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr19:36235200-36235600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr19:36235200-36235600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr19:36235200-36235600	Enhancers	Aorta	Aorta
37	chr19:36235200-36235600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr19:36235200-36235600	Flanking Active TSS	Brain Substantia Nigra	brain
39	chr19:36235200-36235600	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr19:36235200-36235600	Enhancers	Fetal Lung	lung
41	chr19:36235200-36235600	Enhancers	Small Intestine	intestine
42	chr19:36235200-36235600	Flanking Active TSS	Stomach Mucosa	stomach
43	chr19:36235200-36235600	Flanking Active TSS	Thymus	Thymus
44	chr19:36235200-36235600	Flanking Active TSS	A549	lung
45	chr19:36235200-36235600	Enhancers	HMEC	breast
46	chr19:36235200-36235600	Enhancers	HUVEC	blood vessel
47	chr19:36235200-36235800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:36235200-36235800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr19:36235200-36235800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr19:36235200-36235800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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