Variant report

Variant	rs4808969
Chromosome Location	chr19:19647460-19647461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19645771..19647480-chr19:19752306..19754709,2	MCF-7	breast:
2	chr19:19644132..19648148-chr19:19648947..19654743,9	K562	blood:
3	chr19:19643088..19644986-chr19:19645378..19647778,2	MCF-7	breast:
4	chr19:19647280..19649688-chr19:19752870..19754432,2	MCF-7	breast:
5	chr19:19641380..19649124-chr19:19737025..19742358,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160161	Chromatin interaction
ENSG00000064547	Chromatin interaction
ENSG00000089639	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1036215	0.84[AMR][1000 genomes];0.96[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	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11669730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11670687	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11670761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11670775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45631651	0.98[AFR][1000 genomes];1.00[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	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808206	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808970	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55927782	0.93[AMR][1000 genomes];1.00[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	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8101219	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:6 , 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
6	esv1807343	chr19:19639345-19669570	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4808969	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19630600-19651800	Weak transcription	A549	lung
2	chr19:19631000-19647800	Weak transcription	HSMMtube	muscle
3	chr19:19635200-19649200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:19638400-19648800	Weak transcription	GM12878-XiMat	blood
5	chr19:19639000-19648600	Weak transcription	Aorta	Aorta
6	chr19:19639200-19648000	Weak transcription	Ovary	ovary
7	chr19:19639400-19648200	Weak transcription	Primary B cells from cord blood	blood
8	chr19:19639600-19648600	Weak transcription	NHLF	lung
9	chr19:19641000-19648200	Weak transcription	Gastric	stomach
10	chr19:19642200-19650600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:19642400-19648600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr19:19643200-19648200	Weak transcription	Lung	lung
13	chr19:19643400-19648000	Weak transcription	NHDF-Ad	bronchial
14	chr19:19643400-19648400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr19:19643400-19648800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:19643600-19647600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:19643600-19647800	Weak transcription	Fetal Brain Female	brain
18	chr19:19643600-19647800	Weak transcription	Spleen	Spleen
19	chr19:19643600-19648000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr19:19643600-19648000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr19:19643600-19648000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:19643600-19648000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:19643600-19648000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr19:19643600-19648000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr19:19643600-19648000	Weak transcription	Pancreas	Pancrea
26	chr19:19643600-19648200	Weak transcription	Adipose Nuclei	Adipose
27	chr19:19643600-19648200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr19:19643600-19648200	Weak transcription	HMEC	breast
29	chr19:19643600-19648400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:19643600-19648600	Weak transcription	Primary T cells from cord blood	blood
31	chr19:19643600-19648600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr19:19643600-19648600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr19:19643600-19648600	Weak transcription	Brain Anterior Caudate	brain
34	chr19:19643600-19648600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr19:19643600-19648800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr19:19643600-19648800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr19:19643600-19675400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:19643800-19648000	Weak transcription	Colonic Mucosa	Colon
39	chr19:19643800-19648000	Weak transcription	Thymus	Thymus
40	chr19:19643800-19648200	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr19:19643800-19648200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr19:19643800-19648400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr19:19643800-19648600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr19:19643800-19648800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:19643800-19648800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr19:19643800-19648800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr19:19643800-19648800	Weak transcription	Right Atrium	heart
48	chr19:19643800-19649000	Weak transcription	Left Ventricle	heart
49	chr19:19644000-19648200	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr19:19644000-19648600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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