Variant report

Variant	rs2965181
Chromosome Location	chr19:19512317-19512318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19512058..19513091-chr19:19586797..19587941,3	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1036215	0.83[EUR][1000 genomes]
rs10406278	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11085264	0.88[EUR][1000 genomes]
rs11668203	0.96[EUR][1000 genomes]
rs11669558	0.84[EUR][1000 genomes]
rs11669730	0.85[EUR][1000 genomes]
rs11670687	0.88[EUR][1000 genomes]
rs11670761	0.85[EUR][1000 genomes]
rs11670775	0.85[EUR][1000 genomes]
rs11670882	0.83[EUR][1000 genomes]
rs11671253	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1529745	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1557723	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1560687	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16996127	0.86[EUR][1000 genomes]
rs17684164	0.86[EUR][1000 genomes]
rs1989867	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2011503	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2060274	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2060275	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2315023	0.82[AMR][1000 genomes]
rs2315282	0.82[EUR][1000 genomes]
rs2860494	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2905429	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2905433	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2905434	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2916070	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2916072	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2916075	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2965178	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2965179	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2965184	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2965186	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2965187	0.81[AFR][1000 genomes]
rs2965190	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2965195	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2965201	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34487417	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34667451	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4239639	0.89[AMR][1000 genomes]
rs45556231	0.85[EUR][1000 genomes]
rs45631651	0.85[EUR][1000 genomes]
rs4808204	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808205	0.85[EUR][1000 genomes]
rs4808206	0.85[EUR][1000 genomes]
rs4808944	0.82[AMR][1000 genomes]
rs4808951	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4808958	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4808962	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4808968	0.85[EUR][1000 genomes]
rs4808969	0.85[EUR][1000 genomes]
rs4808970	0.84[EUR][1000 genomes]
rs55927782	0.85[EUR][1000 genomes]
rs56280531	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56291054	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56330647	0.86[EUR][1000 genomes]
rs57436187	0.86[AMR][1000 genomes]
rs58074958	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61744761	0.84[EUR][1000 genomes]
rs6511029	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7245689	0.86[EUR][1000 genomes]
rs7250233	0.86[EUR][1000 genomes]
rs7252453	0.84[EUR][1000 genomes]
rs7256028	0.86[EUR][1000 genomes]
rs751857	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs754256	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs756997	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs756999	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8100927	0.85[EUR][1000 genomes]
rs8101219	0.85[EUR][1000 genomes]
rs8102502	0.82[EUR][1000 genomes]
rs8105642	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8110171	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8110250	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8111093	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2965181	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19497600-19515800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:19498000-19515600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:19498400-19513600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr19:19500400-19515400	Weak transcription	Fetal Heart	heart
5	chr19:19500600-19515800	Weak transcription	Right Ventricle	heart
6	chr19:19501200-19514000	Weak transcription	Pancreas	Pancrea
7	chr19:19501400-19513600	Weak transcription	Psoas Muscle	Psoas
8	chr19:19501400-19513800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr19:19505600-19514200	Weak transcription	Small Intestine	intestine
10	chr19:19505800-19513800	Weak transcription	Stomach Mucosa	stomach
11	chr19:19506000-19512800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:19506000-19513600	Weak transcription	Hela-S3	cervix
13	chr19:19506000-19513600	Weak transcription	HepG2	liver
14	chr19:19506000-19513800	Weak transcription	Primary B cells from cord blood	blood
15	chr19:19506000-19513800	Weak transcription	Fetal Intestine Large	intestine
16	chr19:19506000-19514000	Weak transcription	Esophagus	oesophagus
17	chr19:19506000-19515600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:19506000-19515800	Weak transcription	Colonic Mucosa	Colon
19	chr19:19506000-19515800	Weak transcription	Left Ventricle	heart
20	chr19:19506200-19513800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr19:19506200-19513800	Weak transcription	NHEK	skin
22	chr19:19506200-19515600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr19:19506200-19515800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr19:19506200-19515800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr19:19506200-19515800	Weak transcription	Spleen	Spleen
26	chr19:19506400-19515600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr19:19506600-19515400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr19:19507200-19514000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr19:19507400-19514000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr19:19508800-19515600	Weak transcription	Fetal Intestine Small	intestine
31	chr19:19510200-19515800	Weak transcription	Aorta	Aorta
32	chr19:19510800-19513000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr19:19511000-19514000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr19:19511000-19515600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr19:19511200-19512400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr19:19511200-19513600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr19:19511200-19513600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr19:19511200-19513800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr19:19511200-19513800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr19:19511200-19514000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr19:19511200-19514000	Weak transcription	Thymus	Thymus
42	chr19:19511200-19514000	Weak transcription	A549	lung
43	chr19:19511200-19514200	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr19:19511200-19514200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr19:19511200-19515600	Weak transcription	Primary T cells from cord blood	blood
46	chr19:19511200-19515600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr19:19511200-19515600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr19:19511200-19515600	Weak transcription	Brain Hippocampus Middle	brain
49	chr19:19511200-19515800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:19511200-19515800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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