Variant report

Variant	rs7256028
Chromosome Location	chr19:19628240-19628241
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr19:19628070-19628299	K562	blood:	n/a	n/a
2	POLR2A	chr19:19628199-19628259	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:19628195-19628278	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19625745..19628806-chr19:19639215..19643547,5	K562	blood:
2	chr19:19626939..19628497-chr19:19651278..19652936,2	K562	blood:
3	chr19:19626852..19628495-chr19:19842334..19845203,2	MCF-7	breast:
4	chr19:19625365..19628497-chr19:19651436..19653967,3	K562	blood:
5	chr19:19622555..19628571-chr19:19737113..19740295,6	MCF-7	breast:
6	chr19:19625369..19628375-chr19:19648780..19652325,4	MCF-7	breast:

No data

Variant related genes	Relation type
TSSK6	TF binding region
ENSG00000064547	Chromatin interaction
ENSG00000160161	Chromatin interaction
ENSG00000250067	Chromatin interaction
ENSG00000105708	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1036215	0.95[EUR][1000 genomes]
rs10406278	0.83[EUR][1000 genomes]
rs11085264	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11668203	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11669558	0.96[EUR][1000 genomes]
rs11669730	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11670687	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11670761	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11670775	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11670882	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11671253	0.98[EUR][1000 genomes]
rs1529745	0.81[EUR][1000 genomes]
rs1560687	0.90[EUR][1000 genomes]
rs16996127	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17684164	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2060274	0.90[EUR][1000 genomes]
rs2060275	0.89[EUR][1000 genomes]
rs2905434	0.82[EUR][1000 genomes]
rs2916070	0.86[EUR][1000 genomes]
rs2916072	0.90[EUR][1000 genomes]
rs2916075	0.90[EUR][1000 genomes]
rs2965179	0.86[EUR][1000 genomes]
rs2965181	0.86[EUR][1000 genomes]
rs2965184	0.89[EUR][1000 genomes]
rs2965186	0.82[EUR][1000 genomes]
rs34487417	0.84[EUR][1000 genomes]
rs34667451	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs45556231	0.99[EUR][1000 genomes]
rs45631651	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808204	0.98[EUR][1000 genomes]
rs4808205	0.99[EUR][1000 genomes]
rs4808206	0.99[EUR][1000 genomes]
rs4808951	0.89[EUR][1000 genomes]
rs4808958	0.84[EUR][1000 genomes]
rs4808962	0.90[EUR][1000 genomes]
rs4808968	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808969	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808970	0.98[EUR][1000 genomes]
rs55927782	0.99[EUR][1000 genomes]
rs56280531	0.98[EUR][1000 genomes]
rs56291054	0.84[EUR][1000 genomes]
rs56330647	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58074958	0.90[EUR][1000 genomes]
rs61744761	0.96[EUR][1000 genomes]
rs7245689	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7250233	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7252453	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs751857	0.98[EUR][1000 genomes]
rs754256	0.90[EUR][1000 genomes]
rs8100927	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8101219	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8102502	0.95[EUR][1000 genomes]
rs8105642	0.90[EUR][1000 genomes]
rs8110171	0.89[EUR][1000 genomes]
rs8110250	0.90[EUR][1000 genomes]
rs8111093	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7256028	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19626200-19628400	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr19:19626200-19628400	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr19:19626200-19628400	Active TSS	A549	lung
4	chr19:19626200-19628400	Active TSS	HSMM	muscle
5	chr19:19626400-19628400	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr19:19626400-19628400	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr19:19626600-19628400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr19:19626600-19628600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:19626600-19628600	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr19:19626800-19628400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr19:19626800-19628400	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr19:19626800-19628400	Active TSS	Fetal Intestine Small	intestine
13	chr19:19626800-19628800	Active TSS	Muscle Satellite Cultured Cells	--
14	chr19:19627000-19628600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr19:19627200-19628400	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr19:19627200-19628400	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr19:19627400-19628400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:19627600-19628400	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr19:19627600-19628800	Enhancers	Placenta Amnion	Placenta Amnion
20	chr19:19627600-19629000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr19:19627600-19629000	Enhancers	Fetal Brain Male	brain
22	chr19:19627600-19629800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:19627600-19630000	Weak transcription	Aorta	Aorta
24	chr19:19627600-19630400	Weak transcription	Esophagus	oesophagus
25	chr19:19627600-19636200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr19:19627800-19628400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr19:19627800-19628400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr19:19627800-19628400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:19627800-19628400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:19627800-19628400	Enhancers	Left Ventricle	heart
31	chr19:19627800-19628400	Enhancers	Lung	lung
32	chr19:19627800-19628400	Flanking Active TSS	Rectal Smooth Muscle	rectum
33	chr19:19627800-19628400	Flanking Active TSS	Dnd41	blood
34	chr19:19627800-19628600	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr19:19627800-19628600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr19:19627800-19628600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:19627800-19628600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr19:19627800-19628600	Flanking Active TSS	NHEK	skin
39	chr19:19627800-19629000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:19627800-19629000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr19:19627800-19630000	Weak transcription	Brain Substantia Nigra	brain
42	chr19:19627800-19630200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:19628000-19628400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr19:19628000-19628400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr19:19628000-19628400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:19628000-19628400	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr19:19628000-19628400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr19:19628000-19628400	Enhancers	Brain Anterior Caudate	brain
49	chr19:19628000-19628400	Enhancers	Brain Germinal Matrix	brain
50	chr19:19628000-19628400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

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