Variant report

Variant	rs45631651
Chromosome Location	chr19:19638743-19638744
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19637966-19639341	GM12892	blood:	n/a	n/a
2	POLR2A	chr19:19638496-19642169	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:19638376-19638768	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:19638093-19638911	GM12892	blood:	n/a	n/a
5	POLR2A	chr19:19638499-19639196	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:19637987-19641111	HL-60	blood:	n/a	n/a
7	POLR2A	chr19:19638481-19638999	GM12891	blood:	n/a	n/a
8	POLR2A	chr19:19638447-19642194	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr19:19637918-19642166	K562	blood:	n/a	n/a
10	POLR2A	chr19:19638689-19639545	K562	blood:	n/a	n/a
11	SP1	chr19:19638723-19639119	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr19:19638613-19639137	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:19638565-19639607	GM12892	blood:	n/a	n/a
14	POLR2A	chr19:19638629-19639261	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr19:19638725-19639454	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr19:19638581-19638769	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:19638245-19639538	HepG2	liver:	n/a	n/a
18	POLR2A	chr19:19638621-19639488	GM12891	blood:	n/a	n/a
19	POLR2A	chr19:19638461-19641988	K562	blood:	n/a	n/a
20	POLR2A	chr19:19638727-19642069	K562	blood:	n/a	n/a
21	POLR2A	chr19:19638407-19639585	K562	blood:	n/a	n/a
22	POLR2A	chr19:19638658-19639046	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19637478..19643205-chr19:19752988..19755970,5	MCF-7	breast:
2	chr19:19626895..19628424-chr19:19637560..19639397,2	MCF-7	breast:
3	chr19:19429347..19431568-chr19:19636736..19638979,2	K562	blood:
4	chr19:19636166..19641062-chr19:19772143..19775843,4	MCF-7	breast:
5	chr19:19625980..19628021-chr19:19638084..19640231,2	K562	blood:

No data

Variant related genes	Relation type
YJEFN3	TF binding region
ENSG00000178093	Chromatin interaction
ENSG00000258674	Chromatin interaction
ENSG00000105726	Chromatin interaction
ENSG00000105705	Chromatin interaction
ENSG00000089639	Chromatin interaction
ENSG00000186010	Chromatin interaction
ENSG00000129933	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1036215	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10406278	0.82[EUR][1000 genomes]
rs11085264	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11668203	0.89[EUR][1000 genomes]
rs11669558	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11669730	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11670687	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11670761	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11670775	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11670882	0.95[EUR][1000 genomes]
rs11671253	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1560687	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16996127	0.99[EUR][1000 genomes]
rs17684164	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2060274	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2060275	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2905434	0.81[EUR][1000 genomes]
rs2916070	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2916072	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2916075	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2965179	0.85[EUR][1000 genomes]
rs2965181	0.85[EUR][1000 genomes]
rs2965184	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2965186	0.81[EUR][1000 genomes]
rs34487417	0.83[EUR][1000 genomes]
rs34667451	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs45556231	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4808204	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808205	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4808206	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4808951	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808958	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4808962	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808968	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4808969	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4808970	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55927782	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56280531	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56291054	0.83[EUR][1000 genomes]
rs56330647	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58074958	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61744761	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7245689	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7250233	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7252453	0.96[EUR][1000 genomes]
rs7256028	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs751857	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs754256	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8100927	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8101219	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8102502	0.94[EUR][1000 genomes]
rs8105642	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8110171	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8110250	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8111093	0.81[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	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv911307	chr19:19631655-19657143	Bivalent Enhancer Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv911308	chr19:19631655-19663850	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs45631651	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19628000-19640800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:19628200-19642800	Weak transcription	Stomach Mucosa	stomach
3	chr19:19628200-19643000	Weak transcription	HUVEC	blood vessel
4	chr19:19628400-19639200	Weak transcription	Psoas Muscle	Psoas
5	chr19:19628400-19640800	Weak transcription	HMEC	breast
6	chr19:19628400-19642800	Weak transcription	Hela-S3	cervix
7	chr19:19629000-19643600	Weak transcription	Small Intestine	intestine
8	chr19:19630400-19639200	Weak transcription	Fetal Brain Male	brain
9	chr19:19630400-19643000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr19:19630600-19642800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:19630600-19651800	Weak transcription	A549	lung
12	chr19:19630800-19639200	Weak transcription	Brain Substantia Nigra	brain
13	chr19:19630800-19642800	Weak transcription	NHEK	skin
14	chr19:19630800-19643000	Weak transcription	NHDF-Ad	bronchial
15	chr19:19631000-19647800	Weak transcription	HSMMtube	muscle
16	chr19:19632000-19640800	Weak transcription	HSMM	muscle
17	chr19:19633600-19640800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr19:19633800-19638800	Genic enhancers	Fetal Thymus	thymus
19	chr19:19633800-19639200	Strong transcription	Fetal Stomach	stomach
20	chr19:19633800-19640600	Strong transcription	Liver	Liver
21	chr19:19633800-19641000	Strong transcription	Thymus	Thymus
22	chr19:19634000-19639000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr19:19634000-19643000	Strong transcription	Fetal Intestine Small	intestine
24	chr19:19634200-19639400	Strong transcription	Fetal Intestine Large	intestine
25	chr19:19634200-19640200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr19:19634200-19641000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr19:19634400-19640600	Strong transcription	Lung	lung
28	chr19:19634400-19640800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:19634400-19643000	Weak transcription	K562	blood
30	chr19:19634600-19638800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr19:19634600-19639200	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr19:19634600-19640800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr19:19634800-19639200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr19:19634800-19639200	Strong transcription	Ovary	ovary
35	chr19:19634800-19639400	Strong transcription	Stomach Smooth Muscle	stomach
36	chr19:19634800-19640600	Strong transcription	Duodenum Mucosa	Duodenum
37	chr19:19634800-19640800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr19:19634800-19641000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr19:19634800-19641000	Strong transcription	Gastric	stomach
40	chr19:19634800-19641000	Strong transcription	Dnd41	blood
41	chr19:19634800-19642000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr19:19635000-19640400	Strong transcription	Colonic Mucosa	Colon
43	chr19:19635000-19640600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr19:19635000-19640800	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr19:19635200-19649200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr19:19635400-19639400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:19635400-19640600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr19:19635600-19639200	Strong transcription	Placenta	Placenta
49	chr19:19635800-19639200	Strong transcription	Brain Germinal Matrix	brain
50	chr19:19635800-19639400	Strong transcription	Rectal Smooth Muscle	rectum

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