Variant report

Variant	rs754256
Chromosome Location	chr19:19578591-19578592
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19516490..19519551-chr19:19577584..19579824,3	MCF-7	breast:
2	chr19:19577936..19580342-chr19:19585609..19587741,3	MCF-7	breast:
3	chr19:19570376..19575066-chr19:19577857..19582377,6	K562	blood:
4	chr19:19571463..19575965-chr19:19576361..19580794,6	K562	blood:
5	chr19:19578231..19580851-chr19:19582569..19585456,2	K562	blood:
6	chr19:19515118..19519487-chr19:19577388..19580917,4	K562	blood:

Variant related genes	Relation type
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1036215	1.00[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs10406278	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11085264	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11555053	0.81[CEU][hapmap];1.00[TSI][hapmap]
rs11668203	1.00[EUR][1000 genomes]
rs11669558	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11669730	1.00[ASW][hapmap];0.88[CEU][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11670687	0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11670761	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11670775	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11670882	0.94[CEU][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs11671253	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1529745	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1560687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16996127	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs17684164	1.00[CEU][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17751061	0.87[CEU][hapmap];1.00[TSI][hapmap]
rs2010506	0.85[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs2011503	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs2060274	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2060275	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2860494	0.82[EUR][1000 genomes]
rs2905429	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2905433	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2905434	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2916070	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2916072	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2916075	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2965178	0.83[EUR][1000 genomes]
rs2965179	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2965181	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2965184	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2965186	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2965187	0.83[AFR][1000 genomes]
rs2965190	0.83[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap]
rs2965195	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs2965201	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34487417	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34667451	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs45556231	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs45631651	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808204	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4808205	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808206	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808951	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808958	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4808962	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808968	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808969	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808970	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55927782	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56280531	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56291054	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56330647	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58074958	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61744761	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6511027	0.81[CEU][hapmap];0.96[TSI][hapmap]
rs6511029	0.81[EUR][1000 genomes]
rs7245689	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7250233	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7252453	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs7256028	0.90[EUR][1000 genomes]
rs751857	1.00[ASW][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs756997	1.00[CEU][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs8100927	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8101219	0.91[ASW][hapmap];0.96[GIH][hapmap];0.82[LWK][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8102502	0.94[CEU][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs8105642	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8110171	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8110250	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8111093	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs998732	0.81[CEU][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs754256	LSM4	cis	cerebellum	SCAN
rs754256	DDX49	cis	cerebellum	SCAN
rs754256	JUND	cis	parietal	SCAN
rs754256	OCEL1	cis	parietal	SCAN
rs754256	IL12RB1	cis	parietal	SCAN
rs754256	GATAD2A	cis	parietal	SCAN
rs754256	EDG4	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19575000-19578600	Weak transcription	Small Intestine	intestine
2	chr19:19575400-19578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr19:19575600-19581600	ZNF genes & repeats	GM12878-XiMat	blood
4	chr19:19575800-19578600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr19:19575800-19578800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr19:19575800-19578800	Strong transcription	Colonic Mucosa	Colon
7	chr19:19575800-19578800	Weak transcription	Right Atrium	heart
8	chr19:19575800-19579000	Strong transcription	Rectal Mucosa Donor 31	rectum
9	chr19:19575800-19579600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:19575800-19579800	ZNF genes & repeats	Dnd41	blood
11	chr19:19575800-19580000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr19:19575800-19580600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
13	chr19:19575800-19580800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:19575800-19581600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:19576000-19578600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
16	chr19:19576000-19578800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:19576000-19578800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr19:19576000-19578800	Strong transcription	Placenta	Placenta
19	chr19:19576000-19578800	Strong transcription	Osteobl	bone
20	chr19:19576000-19579200	Strong transcription	Stomach Smooth Muscle	stomach
21	chr19:19576000-19579800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:19576200-19578600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
23	chr19:19576200-19578600	Strong transcription	Brain Substantia Nigra	brain
24	chr19:19576200-19579600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:19576200-19580000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:19576200-19580200	ZNF genes & repeats	Thymus	Thymus
27	chr19:19576200-19580600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr19:19576200-19580800	ZNF genes & repeats	Primary B cells from cord blood	blood
29	chr19:19576400-19578600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr19:19576400-19578800	Strong transcription	Brain Angular Gyrus	brain
31	chr19:19576400-19579200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
32	chr19:19576400-19580000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr19:19576400-19580600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
34	chr19:19576400-19580600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
35	chr19:19576400-19580600	ZNF genes & repeats	Fetal Thymus	thymus
36	chr19:19576600-19578600	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr19:19576600-19578800	Strong transcription	Left Ventricle	heart
38	chr19:19576600-19579000	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr19:19576600-19580600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr19:19576600-19580800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr19:19576800-19578800	Strong transcription	Esophagus	oesophagus
42	chr19:19576800-19579000	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr19:19576800-19579400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:19576800-19579800	ZNF genes & repeats	K562	blood
45	chr19:19576800-19579800	ZNF genes & repeats	NHDF-Ad	bronchial
46	chr19:19576800-19580800	ZNF genes & repeats	Fetal Intestine Small	intestine
47	chr19:19577000-19579400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
48	chr19:19577000-19579800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
49	chr19:19577000-19579800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
50	chr19:19577000-19580000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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