Variant report

Variant	rs10408540
Chromosome Location	chr19:55904702-55904703
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:55903449..55905854-chr19:55953578..55955983,2	MCF-7	breast:
2	chr19:55862900..55865359-chr19:55904526..55906118,2	MCF-7	breast:
3	chr19:55682815..55684434-chr19:55902687..55904944,2	K562	blood:
4	chr19:55904255..55905912-chr19:56151359..56153232,2	K562	blood:
5	chr19:55902476..55904959-chr19:56008712..56011316,2	K562	blood:

Variant related genes	Relation type
ENSG00000173581	Chromatin interaction
ENSG00000160471	Chromatin interaction
ENSG00000187902	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000213015	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10403564	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10403989	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10404049	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10404370	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10405802	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10407066	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408088	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408448	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408525	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10410269	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10411984	0.90[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs10415365	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10416908	0.89[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10420818	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs10421889	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423589	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10424289	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10424652	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425107	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425362	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425596	0.86[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs28408730	0.97[AFR][1000 genomes]
rs28536711	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28540780	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28797308	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59698058	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61468173	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73617871	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73617888	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73617896	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73619606	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73619611	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73619651	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
2	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	228 gene(s)	inside rSNPs	diseases
4	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
5	nsv912462	chr19:55845386-55925500	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
6	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
7	nsv912464	chr19:55850269-55921164	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
8	nsv912465	chr19:55854313-55935184	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
9	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
10	nsv544085	chr19:55875808-55911275	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10408540	RPL28	cis	lymphoblastoid	seeQTL
rs10408540	RPL28	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55899200-55913400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:55900200-55918400	Weak transcription	Psoas Muscle	Psoas
3	chr19:55900400-55911800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr19:55900600-55917600	Weak transcription	Stomach Mucosa	stomach
5	chr19:55901000-55917800	Weak transcription	Right Atrium	heart
6	chr19:55901200-55913200	Weak transcription	Small Intestine	intestine
7	chr19:55901400-55912000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:55901600-55911800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr19:55901600-55911800	Weak transcription	HUVEC	blood vessel
10	chr19:55901600-55912000	Weak transcription	HSMM	muscle
11	chr19:55901600-55914400	Weak transcription	Fetal Kidney	kidney
12	chr19:55901800-55905200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr19:55901800-55911800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr19:55901800-55911800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr19:55901800-55916800	Weak transcription	Fetal Brain Male	brain
16	chr19:55902000-55905000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr19:55902000-55905000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:55902000-55911800	Weak transcription	Ovary	ovary
19	chr19:55902000-55912200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr19:55902200-55904800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr19:55902200-55905000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr19:55902200-55910800	Weak transcription	Esophagus	oesophagus
23	chr19:55902200-55911600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr19:55902200-55911800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr19:55902200-55912400	Weak transcription	Colonic Mucosa	Colon
26	chr19:55902200-55917400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr19:55902400-55909200	Weak transcription	GM12878-XiMat	blood
28	chr19:55902400-55911600	Weak transcription	NH-A	brain
29	chr19:55902400-55912000	Weak transcription	Aorta	Aorta
30	chr19:55902600-55911600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:55902600-55911800	Weak transcription	HMEC	breast
32	chr19:55902800-55909600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr19:55902800-55909600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr19:55902800-55911000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr19:55903000-55904800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr19:55903000-55905000	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr19:55903000-55905000	Strong transcription	Stomach Smooth Muscle	stomach
38	chr19:55903000-55909200	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr19:55903000-55910800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr19:55903000-55910800	Weak transcription	Fetal Muscle Leg	muscle
41	chr19:55903000-55911200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr19:55903000-55911400	Weak transcription	Brain Germinal Matrix	brain
43	chr19:55903000-55911800	Weak transcription	Brain Substantia Nigra	brain
44	chr19:55903000-55911800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr19:55903000-55911800	Weak transcription	NHDF-Ad	bronchial
46	chr19:55903000-55912000	Weak transcription	Brain Angular Gyrus	brain
47	chr19:55903000-55912000	Weak transcription	Gastric	stomach
48	chr19:55903000-55912000	Weak transcription	Pancreas	Pancrea
49	chr19:55903000-55913200	Weak transcription	Fetal Lung	lung
50	chr19:55903000-55914000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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