Variant report

Variant	rs2905433
Chromosome Location	chr19:19490203-19490204
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19485925..19490752-chr19:19494037..19501324,14	MCF-7	breast:
2	chr19:19489733..19491954-chr19:19497664..19499602,2	K562	blood:
3	chr19:19487332..19490283-chr19:19515104..19517573,4	MCF-7	breast:
4	chr19:19484073..19490340-chr19:19494015..19501154,14	MCF-7	breast:
5	chr19:19487435..19490372-chr19:19555512..19558220,2	MCF-7	breast:
6	chr19:19488930..19490587-chr19:19548846..19551529,2	K562	blood:
7	chr19:19487227..19491094-chr19:19586686..19591214,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10406278	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11668203	0.85[EUR][1000 genomes]
rs1529745	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1557723	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1560687	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1989867	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2011503	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2060274	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2060275	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2315282	0.88[EUR][1000 genomes]
rs2860494	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2905429	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2905434	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2916070	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2916072	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2916075	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2965178	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2965179	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2965181	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2965184	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2965186	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2965187	0.87[AFR][1000 genomes]
rs2965190	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2965195	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2965201	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34487417	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4239639	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4808951	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4808958	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4808962	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs56291054	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57436187	0.80[AMR][1000 genomes]
rs58074958	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6511029	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs754256	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs756997	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs756999	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8105642	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8110171	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs8110250	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8111093	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[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
rs2905433	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 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	chr19:19482600-19493200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr19:19486400-19491800	Weak transcription	GM12878-XiMat	blood
4	chr19:19486400-19495400	Weak transcription	Primary B cells from peripheral blood	blood
5	chr19:19486400-19495600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:19488200-19492400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr19:19488600-19491000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr19:19488600-19491800	Weak transcription	Small Intestine	intestine
9	chr19:19488800-19492800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:19488800-19495400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr19:19488800-19495400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:19488800-19495400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr19:19488800-19495400	Weak transcription	Fetal Muscle Leg	muscle
14	chr19:19488800-19495400	Weak transcription	Gastric	stomach
15	chr19:19489000-19490400	Weak transcription	Brain Hippocampus Middle	brain
16	chr19:19489000-19490400	Weak transcription	Brain Substantia Nigra	brain
17	chr19:19489000-19490800	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr19:19489000-19491600	Weak transcription	Stomach Mucosa	stomach
19	chr19:19489000-19491800	Weak transcription	Esophagus	oesophagus
20	chr19:19489000-19491800	Weak transcription	HUVEC	blood vessel
21	chr19:19489000-19492800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr19:19489000-19495200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr19:19489000-19495200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr19:19489000-19495200	Weak transcription	A549	lung
25	chr19:19489000-19495400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr19:19489000-19495400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:19489000-19495400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr19:19489000-19495400	Weak transcription	Adipose Nuclei	Adipose
29	chr19:19489000-19495400	Weak transcription	Colon Smooth Muscle	Colon
30	chr19:19489000-19495400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr19:19489000-19495400	Weak transcription	Hela-S3	cervix
32	chr19:19489000-19495400	Weak transcription	Osteobl	bone
33	chr19:19489000-19495600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr19:19489000-19495600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr19:19489000-19495600	Weak transcription	Fetal Lung	lung
36	chr19:19489200-19491200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr19:19489200-19491800	Weak transcription	Fetal Intestine Small	intestine
38	chr19:19489200-19491800	Weak transcription	Pancreas	Pancrea
39	chr19:19489200-19491800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr19:19489200-19492400	Enhancers	Placenta	Placenta
41	chr19:19489200-19494800	Weak transcription	Fetal Muscle Trunk	muscle
42	chr19:19489200-19495200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr19:19489200-19495400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr19:19489200-19495400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr19:19489200-19495400	Weak transcription	NHEK	skin
46	chr19:19489200-19495600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr19:19489200-19495600	Weak transcription	HMEC	breast
48	chr19:19489200-19496000	Weak transcription	Spleen	Spleen
49	chr19:19489400-19490800	Enhancers	HepG2	liver
50	chr19:19489400-19495600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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