Variant report

Variant	rs10412176
Chromosome Location	chr19:19689164-19689165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19689040..19691188-chr19:19737339..19740827,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000064547	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1036215	1.00[YRI][hapmap]
rs10417140	1.00[YRI][hapmap]
rs11668721	1.00[YRI][hapmap]
rs4808973	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56159542	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7250602	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7250942	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8103992	0.90[EUR][1000 genomes]
rs8108659	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8113006	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
rs10412176	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19671600-19701800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr19:19672000-19704800	Weak transcription	Brain Angular Gyrus	brain
3	chr19:19674200-19689200	Weak transcription	Brain Substantia Nigra	brain
4	chr19:19674200-19690600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr19:19674200-19690800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr19:19674200-19691000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr19:19674200-19699800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr19:19674400-19690600	Weak transcription	Stomach Mucosa	stomach
9	chr19:19676200-19701600	Weak transcription	GM12878-XiMat	blood
10	chr19:19678800-19693000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr19:19679800-19690600	Weak transcription	NHEK	skin
12	chr19:19680400-19689200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr19:19680400-19690400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr19:19681200-19689200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr19:19681200-19701600	Weak transcription	NHLF	lung
16	chr19:19681400-19690000	Weak transcription	Lung	lung
17	chr19:19681400-19690600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr19:19681400-19690600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr19:19681400-19690600	Weak transcription	Gastric	stomach
20	chr19:19681400-19690800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr19:19681400-19701600	Weak transcription	Fetal Lung	lung
22	chr19:19681600-19690800	Weak transcription	Primary T cells from cord blood	blood
23	chr19:19681600-19693000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:19681600-19701600	Weak transcription	Esophagus	oesophagus
25	chr19:19681600-19703200	Weak transcription	Dnd41	blood
26	chr19:19681800-19690600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr19:19681800-19691000	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr19:19681800-19692800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr19:19682000-19690400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr19:19682000-19690400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:19682000-19690600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:19682000-19692800	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr19:19682000-19702200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr19:19682200-19692000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr19:19682400-19692800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr19:19682600-19692800	Weak transcription	Spleen	Spleen
37	chr19:19682600-19700600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr19:19686600-19700600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr19:19686800-19689200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr19:19686800-19689200	Weak transcription	Fetal Brain Male	brain
41	chr19:19686800-19690200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr19:19687000-19689200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr19:19687000-19689600	Weak transcription	Fetal Stomach	stomach
44	chr19:19687000-19693000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr19:19687000-19701600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr19:19688400-19691000	Enhancers	Brain Germinal Matrix	brain
47	chr19:19688400-19691000	Enhancers	Fetal Muscle Trunk	muscle
48	chr19:19688400-19692800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr19:19688400-19699000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr19:19688600-19691000	Enhancers	Fetal Muscle Leg	muscle

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