Variant report

Variant	rs10221489
Chromosome Location	chr19:18826975-18826976
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18810589..18812335-chr19:18824171..18827003,2	MCF-7	breast:
2	chr19:18809327..18811934-chr19:18826162..18828018,2	MCF-7	breast:
3	chr19:18826396..18828124-chr19:18830116..18832306,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10412858	0.81[CHB][hapmap]
rs10419226	0.90[CHB][hapmap]
rs10423674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10854003	0.85[CHB][hapmap]
rs11668545	0.89[JPT][hapmap]
rs11668587	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12462498	0.89[JPT][hapmap]
rs1473116	0.85[CHB][hapmap]
rs2023878	0.89[JPT][hapmap]
rs3829671	0.82[CHB][hapmap]
rs60021783	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6510995	0.82[CHB][hapmap]
rs7246437	0.81[CHB][hapmap]
rs8100824	0.85[CHB][hapmap]
rs8102046	0.86[CHB][hapmap]
rs876982	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv960927	chr19:18808010-18837082	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10221489	PBX4	cis	multi-tissue	Pritchard

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18812000-18844200	Weak transcription	Fetal Kidney	kidney
2	chr19:18812400-18827600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:18812400-18827800	Weak transcription	Brain Germinal Matrix	brain
4	chr19:18812600-18828200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr19:18818000-18836600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr19:18819000-18844000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr19:18820400-18833000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr19:18820400-18837000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr19:18820400-18847200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr19:18820600-18846600	Weak transcription	Esophagus	oesophagus
11	chr19:18820800-18828200	Weak transcription	Gastric	stomach
12	chr19:18820800-18832800	Weak transcription	HSMM	muscle
13	chr19:18821200-18827800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr19:18821200-18828400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr19:18821200-18828600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr19:18821200-18829000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:18821200-18833000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr19:18821200-18834400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr19:18821200-18844000	Weak transcription	Colonic Mucosa	Colon
20	chr19:18821200-18860600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:18821200-18861000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr19:18821200-18864800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr19:18821400-18828000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr19:18821800-18827000	Strong transcription	Fetal Intestine Small	intestine
25	chr19:18822000-18833000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:18822200-18828200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:18822200-18828400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:18822200-18830600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr19:18822400-18833400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr19:18822400-18835600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr19:18822600-18827400	Weak transcription	Spleen	Spleen
32	chr19:18822600-18827600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:18822600-18827800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr19:18822600-18828400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr19:18822600-18830000	Weak transcription	Fetal Intestine Large	intestine
36	chr19:18822600-18836400	Weak transcription	Adipose Nuclei	Adipose
37	chr19:18822600-18843800	Weak transcription	Colon Smooth Muscle	Colon
38	chr19:18822600-18844000	Weak transcription	NHLF	lung
39	chr19:18822800-18827000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:18822800-18827600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr19:18822800-18828000	Weak transcription	Placenta	Placenta
42	chr19:18822800-18836800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr19:18823600-18827000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr19:18823800-18827000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr19:18824200-18846600	Weak transcription	Pancreas	Pancrea
46	chr19:18824400-18829000	Weak transcription	Brain Anterior Caudate	brain
47	chr19:18824400-18829400	Weak transcription	Brain Angular Gyrus	brain
48	chr19:18824400-18829800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr19:18824400-18833000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:18824600-18827000	Weak transcription	Aorta	Aorta

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