Variant report

Variant	rs10406278
Chromosome Location	chr19:19494725-19494726
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19494550..19497983-chr19:19513188..19518336,8	MCF-7	breast:
2	chr19:19491673..19504307-chr19:19513999..19523684,33	K562	blood:
3	chr19:19483095..19487397-chr19:19491404..19494790,5	K562	blood:
4	chr19:19492268..19501550-chr19:19512499..19523684,29	K562	blood:
5	chr19:19483132..19485532-chr19:19492429..19494779,2	K562	blood:

Variant related genes	Relation type
ENSG00000167491	Chromatin interaction
ENSG00000267234	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1036215	0.80[EUR][1000 genomes]
rs11085264	0.85[EUR][1000 genomes]
rs11668203	0.93[EUR][1000 genomes]
rs11669558	0.81[EUR][1000 genomes]
rs11669730	0.82[EUR][1000 genomes]
rs11670687	0.85[EUR][1000 genomes]
rs11670761	0.82[EUR][1000 genomes]
rs11670775	0.82[EUR][1000 genomes]
rs11671253	0.85[EUR][1000 genomes]
rs1529745	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1557723	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1560687	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs16996127	0.83[EUR][1000 genomes]
rs17684164	0.83[EUR][1000 genomes]
rs1989867	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2011503	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2060274	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2060275	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2315023	0.84[AMR][1000 genomes]
rs2315282	0.82[EUR][1000 genomes]
rs2860494	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2905429	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2905433	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2905434	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2916070	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2916072	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2916075	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2965178	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2965179	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2965181	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2965184	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2965186	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2965187	0.88[AFR][1000 genomes]
rs2965190	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2965195	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2965201	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34487417	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34667451	0.85[EUR][1000 genomes]
rs4239639	0.82[AMR][1000 genomes]
rs45556231	0.82[EUR][1000 genomes]
rs45631651	0.82[EUR][1000 genomes]
rs4808204	0.85[EUR][1000 genomes]
rs4808205	0.82[EUR][1000 genomes]
rs4808206	0.82[EUR][1000 genomes]
rs4808944	0.84[AMR][1000 genomes]
rs4808951	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4808958	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4808962	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4808968	0.82[EUR][1000 genomes]
rs4808969	0.82[EUR][1000 genomes]
rs4808970	0.83[EUR][1000 genomes]
rs55927782	0.82[EUR][1000 genomes]
rs56280531	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs56291054	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56330647	0.83[EUR][1000 genomes]
rs57436187	0.88[AMR][1000 genomes]
rs58074958	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs61744761	0.81[EUR][1000 genomes]
rs6511029	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7245689	0.83[EUR][1000 genomes]
rs7250233	0.83[EUR][1000 genomes]
rs7252453	0.81[EUR][1000 genomes]
rs7256028	0.83[EUR][1000 genomes]
rs751857	0.85[EUR][1000 genomes]
rs754256	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs756997	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs756999	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8100927	0.82[EUR][1000 genomes]
rs8101219	0.82[EUR][1000 genomes]
rs8105642	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs8110171	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs8110250	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs8111093	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[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	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	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
3	nsv1056419	chr19:19421218-19510611	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10406278	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19478800-19495800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:19486400-19495400	Weak transcription	Primary B cells from peripheral blood	blood
3	chr19:19486400-19495600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:19488800-19495400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:19488800-19495400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:19488800-19495400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr19:19488800-19495400	Weak transcription	Fetal Muscle Leg	muscle
8	chr19:19488800-19495400	Weak transcription	Gastric	stomach
9	chr19:19489000-19495200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr19:19489000-19495200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr19:19489000-19495200	Weak transcription	A549	lung
12	chr19:19489000-19495400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr19:19489000-19495400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:19489000-19495400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr19:19489000-19495400	Weak transcription	Adipose Nuclei	Adipose
16	chr19:19489000-19495400	Weak transcription	Colon Smooth Muscle	Colon
17	chr19:19489000-19495400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr19:19489000-19495400	Weak transcription	Hela-S3	cervix
19	chr19:19489000-19495400	Weak transcription	Osteobl	bone
20	chr19:19489000-19495600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr19:19489000-19495600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr19:19489000-19495600	Weak transcription	Fetal Lung	lung
23	chr19:19489200-19494800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr19:19489200-19495200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr19:19489200-19495400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr19:19489200-19495400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr19:19489200-19495400	Weak transcription	NHEK	skin
28	chr19:19489200-19495600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr19:19489200-19495600	Weak transcription	HMEC	breast
30	chr19:19489200-19496000	Weak transcription	Spleen	Spleen
31	chr19:19489400-19495600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr19:19489800-19495200	Weak transcription	Fetal Heart	heart
33	chr19:19490800-19495200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr19:19490800-19495600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr19:19491000-19495400	Weak transcription	Brain Hippocampus Middle	brain
36	chr19:19491200-19495400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr19:19491400-19494800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr19:19492000-19495200	Weak transcription	Colonic Mucosa	Colon
39	chr19:19492200-19495200	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr19:19492200-19495400	Weak transcription	Primary B cells from cord blood	blood
41	chr19:19492200-19495400	Weak transcription	Fetal Intestine Small	intestine
42	chr19:19492200-19495400	Weak transcription	Lung	lung
43	chr19:19492400-19495400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr19:19492400-19495400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr19:19492400-19495600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr19:19492600-19495200	Weak transcription	HUVEC	blood vessel
47	chr19:19492600-19495400	Enhancers	K562	blood
48	chr19:19492600-19495600	Weak transcription	Brain Substantia Nigra	brain
49	chr19:19492600-19495600	Weak transcription	Small Intestine	intestine
50	chr19:19492800-19495600	Enhancers	Placenta	Placenta

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