Variant report

Variant	rs1552783
Chromosome Location	chr8:19552218-19552219
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:19552184..19554316-chr8:19556580..19558198,2	MCF-7	breast:
2	chr8:19534245..19536815-chr8:19550846..19553257,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253270	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11778161	0.95[CEU][hapmap];0.87[YRI][hapmap];0.87[EUR][1000 genomes]
rs1552776	0.95[CEU][hapmap];0.87[YRI][hapmap];0.87[EUR][1000 genomes]
rs17481277	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17481361	1.00[CEU][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1907800	0.81[EUR][1000 genomes]
rs3735958	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6586858	0.81[EUR][1000 genomes]
rs6985467	0.81[EUR][1000 genomes]
rs6992467	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7812740	0.87[EUR][1000 genomes]
rs7843349	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[GIH][hapmap];0.87[TSI][hapmap];0.81[YRI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv948861	chr8:19199688-19609029	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv949304	chr8:19199688-19625912	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv890625	chr8:19368697-19799641	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv890627	chr8:19389865-19561997	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1021575	chr8:19430653-19623452	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1025271	chr8:19435147-19574969	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1021731	chr8:19515149-19643313	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv465602	chr8:19536015-19555398	Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv610757	chr8:19536015-19555398	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv465603	chr8:19537084-19555398	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv465604	chr8:19537084-19555398	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv465606	chr8:19537084-19555398	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv465607	chr8:19537084-19555398	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv470203	chr8:19537084-19555398	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv610758	chr8:19537084-19555398	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv528523	chr8:19546696-19555398	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1552783	INTS10	cis	cerebellum	SCAN
rs1552783	PEBP4	cis	cerebellum	SCAN
rs1552783	CSGALNACT1	cis	Whole Blood	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19541000-19554200	Weak transcription	Brain Substantia Nigra	brain
2	chr8:19541000-19567400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr8:19548200-19553800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr8:19548200-19559200	Enhancers	Primary B cells from peripheral blood	blood
5	chr8:19548800-19554200	Weak transcription	Colonic Mucosa	Colon
6	chr8:19549200-19554400	Weak transcription	Brain Anterior Caudate	brain
7	chr8:19549400-19552400	Weak transcription	Gastric	stomach
8	chr8:19549600-19553600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr8:19549600-19553800	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr8:19549600-19554000	Weak transcription	Placenta	Placenta
11	chr8:19549600-19554200	Weak transcription	Brain Angular Gyrus	brain
12	chr8:19549600-19555200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr8:19549800-19553200	Enhancers	Primary T cells from cord blood	blood
14	chr8:19549800-19553600	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr8:19550000-19552600	Enhancers	Left Ventricle	heart
16	chr8:19550000-19553800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr8:19550200-19553600	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr8:19550200-19553800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr8:19550200-19554200	Enhancers	Primary T cells fromperipheralblood	blood
20	chr8:19550200-19556000	Enhancers	Fetal Thymus	thymus
21	chr8:19550200-19558600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr8:19550200-19558600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr8:19550400-19553800	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr8:19550400-19558400	Enhancers	Primary hematopoietic stem cells	blood
25	chr8:19550600-19554000	Weak transcription	Spleen	Spleen
26	chr8:19550800-19553600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr8:19550800-19553600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr8:19551000-19552400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr8:19551000-19554600	Enhancers	Fetal Brain Male	brain
30	chr8:19551000-19556000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr8:19551200-19554000	Weak transcription	Esophagus	oesophagus
32	chr8:19551200-19554000	Weak transcription	A549	lung
33	chr8:19551400-19554000	Weak transcription	Lung	lung
34	chr8:19551400-19554600	Weak transcription	Colon Smooth Muscle	Colon
35	chr8:19551600-19552600	Enhancers	Fetal Brain Female	brain
36	chr8:19551600-19554000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr8:19551800-19552400	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr8:19551800-19553800	Enhancers	Fetal Lung	lung
39	chr8:19551800-19554000	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr8:19551800-19554000	Enhancers	Fetal Stomach	stomach
41	chr8:19551800-19558200	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr8:19552000-19552600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr8:19552000-19552600	Enhancers	Fetal Muscle Leg	muscle
44	chr8:19552000-19552600	Enhancers	Ovary	ovary
45	chr8:19552000-19552600	Enhancers	Right Ventricle	heart
46	chr8:19552000-19552600	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr8:19552000-19552600	Enhancers	Small Intestine	intestine
48	chr8:19552000-19552600	Enhancers	Stomach Smooth Muscle	stomach
49	chr8:19552000-19553000	Enhancers	Primary B cells from cord blood	blood
50	chr8:19552000-19553000	Enhancers	Pancreas	Pancrea

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