Variant report

Variant	rs28633929
Chromosome Location	chr19:36151514-36151515
allele	A/G
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	chr19:36151340-36151816	K562	blood:	n/a	n/a
2	POLR2A	chr19:36150426-36151547	K562	blood:	n/a	n/a
3	POLR2A	chr19:36151336-36151596	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:36150261-36152652	K562	blood:	n/a	n/a
5	POLR2A	chr19:36150790-36151590	K562	blood:	n/a	n/a
6	CEBPB	chr19:36151425-36151573	K562	blood:	n/a	n/a
7	POLR2A	chr19:36151116-36152536	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36137102..36140091-chr19:36148183..36153903,5	MCF-7	breast:
2	chr19:36133300..36135644-chr19:36148986..36151706,2	MCF-7	breast:

Variant related genes	Relation type
RN7SL765P	TF binding region
ENSG00000126267	Chromatin interaction
ENSG00000105672	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10413852	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12104249	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12459073	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12459634	0.82[TSI][hapmap]
rs12461285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs12461333	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2234371	0.82[EUR][1000 genomes]
rs2871921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs34031911	0.82[EUR][1000 genomes]
rs35209304	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35729071	0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs3848662	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs56170803	0.90[ASN][1000 genomes]
rs56189160	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62109452	0.82[EUR][1000 genomes]
rs62109998	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7249885	0.84[EUR][1000 genomes]
rs7254601	0.82[JPT][hapmap];0.81[TSI][hapmap]
rs73048504	0.82[EUR][1000 genomes]
rs8106959	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs9304874	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv543995	chr19:36139204-36203592	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs28633929	U2AF1L4	cis	Muscle Skeletal	GTEx
rs28633929	TMEM149	Cis_1M	lymphoblastoid	RTeQTL
rs28633929	RN7SL765P	cis	Muscle Skeletal	GTEx
rs28633929	U2AF1L4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36140000-36154000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:36140200-36152800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:36140400-36151600	Weak transcription	Stomach Mucosa	stomach
4	chr19:36140400-36164000	Weak transcription	Right Atrium	heart
5	chr19:36140600-36153800	Strong transcription	Fetal Intestine Small	intestine
6	chr19:36140600-36157200	Strong transcription	Fetal Stomach	stomach
7	chr19:36140800-36153800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr19:36141000-36155600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr19:36141000-36157000	Strong transcription	Fetal Muscle Trunk	muscle
10	chr19:36141400-36156800	Strong transcription	Spleen	Spleen
11	chr19:36141400-36157200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:36141600-36152600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:36141800-36152800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr19:36141800-36153000	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr19:36141800-36154000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr19:36141800-36156800	Strong transcription	Fetal Thymus	thymus
17	chr19:36142000-36152200	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr19:36142200-36156800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:36142200-36156800	Strong transcription	Left Ventricle	heart
20	chr19:36142200-36157800	Weak transcription	Fetal Heart	heart
21	chr19:36142400-36152800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr19:36142800-36152800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr19:36142800-36157200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr19:36143000-36153800	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr19:36143600-36156000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr19:36144400-36156800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr19:36144600-36152200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr19:36144600-36152600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr19:36144600-36152800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr19:36144600-36153800	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr19:36144600-36155000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr19:36144600-36155400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:36144600-36156400	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr19:36144600-36156600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr19:36144600-36156800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr19:36144600-36156800	Strong transcription	Primary B cells from peripheral blood	blood
37	chr19:36144600-36157200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr19:36144600-36157600	Strong transcription	Thymus	Thymus
39	chr19:36144800-36151600	Strong transcription	Rectal Smooth Muscle	rectum
40	chr19:36144800-36152600	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr19:36144800-36152600	Strong transcription	Brain Cingulate Gyrus	brain
42	chr19:36144800-36152600	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr19:36144800-36153600	Strong transcription	Brain Angular Gyrus	brain
44	chr19:36144800-36156600	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr19:36144800-36156600	Strong transcription	Gastric	stomach
46	chr19:36144800-36156800	Strong transcription	Brain Anterior Caudate	brain
47	chr19:36144800-36157000	Strong transcription	Fetal Muscle Leg	muscle
48	chr19:36145200-36152600	Strong transcription	Esophagus	oesophagus
49	chr19:36145400-36152800	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr19:36145800-36157200	Strong transcription	Primary T cells fromperipheralblood	blood

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