Variant report

Variant	rs7245689
Chromosome Location	chr19:19629530-19629531
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19628992..19634294-chr19:19634431..19640068,9	K562	blood:
2	chr19:19626638..19628267-chr19:19629000..19631454,2	MCF-7	breast:
3	chr19:19627013..19628859-chr19:19629053..19631884,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186010	Chromatin interaction
ENSG00000250067	Chromatin interaction
ENSG00000258674	Chromatin interaction
ENSG00000178093	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	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10406278	0.83[EUR][1000 genomes]
rs11085264	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11668203	0.90[EUR][1000 genomes]
rs11669558	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11669730	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11670687	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11670761	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11670775	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11670882	0.96[EUR][1000 genomes]
rs11671253	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1529745	0.81[EUR][1000 genomes]
rs1560687	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16996127	1.00[EUR][1000 genomes]
rs17684164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2060274	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2060275	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2905434	0.82[EUR][1000 genomes]
rs2916070	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2916072	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2916075	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2965179	0.86[EUR][1000 genomes]
rs2965181	0.86[EUR][1000 genomes]
rs2965184	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2965186	0.82[EUR][1000 genomes]
rs34487417	0.84[EUR][1000 genomes]
rs34667451	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs45556231	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs45631651	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808204	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4808205	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808206	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808951	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808958	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4808962	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4808968	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808969	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808970	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55927782	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56280531	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56291054	0.84[EUR][1000 genomes]
rs56330647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58074958	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61744761	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7250233	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7252453	0.97[EUR][1000 genomes]
rs7256028	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs751857	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs754256	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8100927	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8101219	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8102502	0.95[EUR][1000 genomes]
rs8105642	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8110171	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8110250	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];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
rs7245689	SF4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19627600-19629800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr19:19627600-19630000	Weak transcription	Aorta	Aorta
3	chr19:19627600-19630400	Weak transcription	Esophagus	oesophagus
4	chr19:19627600-19636200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:19627800-19630000	Weak transcription	Brain Substantia Nigra	brain
6	chr19:19627800-19630200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:19628000-19630000	Enhancers	Primary T cells fromperipheralblood	blood
8	chr19:19628000-19630200	Weak transcription	HSMMtube	muscle
9	chr19:19628000-19634800	Weak transcription	Fetal Kidney	kidney
10	chr19:19628000-19635000	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr19:19628000-19636000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr19:19628000-19638000	Weak transcription	Fetal Lung	lung
13	chr19:19628000-19640800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr19:19628200-19629800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr19:19628200-19629800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:19628200-19630000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr19:19628200-19630000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr19:19628200-19630000	Weak transcription	NHLF	lung
19	chr19:19628200-19630200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr19:19628200-19630200	Weak transcription	NHDF-Ad	bronchial
21	chr19:19628200-19630400	Enhancers	Brain Cingulate Gyrus	brain
22	chr19:19628200-19631600	Weak transcription	NH-A	brain
23	chr19:19628200-19636200	Weak transcription	Fetal Heart	heart
24	chr19:19628200-19636200	Weak transcription	Right Atrium	heart
25	chr19:19628200-19642800	Weak transcription	Stomach Mucosa	stomach
26	chr19:19628200-19643000	Weak transcription	HUVEC	blood vessel
27	chr19:19628400-19629800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:19628400-19629800	Weak transcription	Fetal Thymus	thymus
29	chr19:19628400-19629800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr19:19628400-19630000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:19628400-19630000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr19:19628400-19630000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr19:19628400-19630000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr19:19628400-19630000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:19628400-19630000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr19:19628400-19630000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr19:19628400-19630000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr19:19628400-19630000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr19:19628400-19630000	Weak transcription	Brain Anterior Caudate	brain
40	chr19:19628400-19630000	Weak transcription	Brain Germinal Matrix	brain
41	chr19:19628400-19630000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr19:19628400-19630000	Weak transcription	Fetal Intestine Large	intestine
43	chr19:19628400-19630000	Weak transcription	Placenta	Placenta
44	chr19:19628400-19630000	Weak transcription	Left Ventricle	heart
45	chr19:19628400-19630000	Weak transcription	Lung	lung
46	chr19:19628400-19630000	Weak transcription	Ovary	ovary
47	chr19:19628400-19630000	Weak transcription	Right Ventricle	heart
48	chr19:19628400-19630000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr19:19628400-19630000	Weak transcription	Spleen	Spleen
50	chr19:19628400-19630200	Weak transcription	Colonic Mucosa	Colon

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