Variant report

Variant	rs28656784
Chromosome Location	chr19:36234489-36234490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36207379..36214815-chr19:36234227..36241330,25	MCF-7	breast:
2	chr19:36035683..36038067-chr19:36234353..36237102,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-U2AF1L4-1	chr19:36233430-36234805	NONHSAT065899
2	lnc-U2AF1L4-1	chr19:36233434-36234805	NONHSAT065902

Variant related genes	Relation type
ENSG00000272333	Chromatin interaction
ENSG00000105677	Chromatin interaction
ENSG00000236144	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10401156	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10402601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10402837	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11549030	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459634	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2239947	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293686	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];1.00[EUR][1000 genomes]
rs34031911	0.82[AFR][1000 genomes]
rs35729071	0.80[EUR][1000 genomes]
rs3746277	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3848662	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3848665	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62112162	0.85[EUR][1000 genomes]
rs7260184	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[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
rs28656784	U2AF1L4	cis	Muscle Skeletal	GTEx
rs28656784	U2AF1L4	Cis_1M	lymphoblastoid	RTeQTL
rs28656784	U2AF1L4	cis	lung	GTEx
rs28656784	U2AF1L4	cis	Esophagus Muscularis	GTEx
rs28656784	U2AF1L4	cis	Whole Blood	GTEx
rs28656784	TMEM149	Cis_1M	lymphoblastoid	RTeQTL
rs28656784	LIN37	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36231400-36235200	Weak transcription	Fetal Heart	heart
2	chr19:36232000-36234800	Weak transcription	Gastric	stomach
3	chr19:36232200-36234800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:36232200-36234800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:36232200-36234800	Weak transcription	Fetal Kidney	kidney
6	chr19:36232200-36234800	Weak transcription	Right Ventricle	heart
7	chr19:36232200-36234800	Weak transcription	Hela-S3	cervix
8	chr19:36232200-36235000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr19:36232200-36235000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr19:36232200-36235000	Weak transcription	Fetal Brain Male	brain
11	chr19:36232200-36235000	Weak transcription	Stomach Mucosa	stomach
12	chr19:36232200-36235000	Weak transcription	Osteobl	bone
13	chr19:36232200-36235200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr19:36232200-36235200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr19:36232200-36235200	Weak transcription	Aorta	Aorta
16	chr19:36232200-36235200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr19:36232200-36235200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr19:36232200-36235200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr19:36232200-36235200	Weak transcription	HMEC	breast
20	chr19:36232200-36235200	Weak transcription	HUVEC	blood vessel
21	chr19:36232200-36235200	Weak transcription	NH-A	brain
22	chr19:36232200-36235200	Weak transcription	NHDF-Ad	bronchial
23	chr19:36232400-36234800	Weak transcription	Right Atrium	heart
24	chr19:36232400-36235000	Weak transcription	Fetal Brain Female	brain
25	chr19:36232400-36235200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr19:36232400-36235200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr19:36232400-36235200	Weak transcription	Small Intestine	intestine
28	chr19:36232400-36235400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr19:36232400-36235400	Weak transcription	Psoas Muscle	Psoas
30	chr19:36232600-36234800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:36232600-36234800	Weak transcription	Brain Germinal Matrix	brain
32	chr19:36232600-36235000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr19:36232600-36235000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr19:36232600-36235200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr19:36232600-36235200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr19:36232600-36235200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr19:36232600-36235200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr19:36232800-36235000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr19:36232800-36235200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr19:36232800-36235400	Strong transcription	Fetal Intestine Small	intestine
41	chr19:36233000-36234800	Strong transcription	NHEK	skin
42	chr19:36233000-36235000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:36233000-36235000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:36233000-36235000	Strong transcription	HSMMtube	muscle
45	chr19:36233000-36235000	Strong transcription	NHLF	lung
46	chr19:36233000-36235200	Genic enhancers	Brain Hippocampus Middle	brain
47	chr19:36233000-36235200	Genic enhancers	Fetal Muscle Trunk	muscle
48	chr19:36233000-36235200	Strong transcription	Fetal Stomach	stomach
49	chr19:36233000-36235400	Genic enhancers	Fetal Muscle Leg	muscle
50	chr19:36233200-36234800	Strong transcription	Brain Anterior Caudate	brain

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