Variant report

Variant	rs4244455
Chromosome Location	chr8:19527536-19527537
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:19521485..19523580-chr8:19526746..19529079,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10087146	1.00[ASW][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10098471	0.84[AMR][1000 genomes]
rs10107740	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11992703	0.82[CHB][hapmap]
rs1492644	1.00[ASW][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes]
rs1492645	0.82[CEU][hapmap];0.91[AMR][1000 genomes]
rs1552777	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17091532	1.00[ASW][hapmap]
rs4922081	0.82[CHB][hapmap]
rs4922082	0.82[CHB][hapmap]
rs4922083	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6586856	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs6586857	0.93[AMR][1000 genomes]
rs7016714	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7016838	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[AMR][1000 genomes];0.89[EUR][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	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	nsv6106	chr8:19499554-19544249	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	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
10	nsv890628	chr8:19527536-19540966	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4244455	SLC18A1	cis	cerebellum	SCAN
rs4244455	ChGn	cis	multi-tissue	Pritchard
rs4244455	SLC39A14	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19520200-19529000	Enhancers	Primary B cells from cord blood	blood
2	chr8:19520400-19527600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr8:19520400-19528600	Weak transcription	Brain Angular Gyrus	brain
4	chr8:19520400-19530400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr8:19520400-19539000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr8:19520400-19539400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr8:19520400-19539600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr8:19520600-19528400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr8:19520600-19528600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr8:19520600-19528600	Weak transcription	Lung	lung
11	chr8:19520600-19538800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr8:19520600-19538800	Weak transcription	Esophagus	oesophagus
13	chr8:19520600-19538800	Weak transcription	Gastric	stomach
14	chr8:19521800-19527600	Weak transcription	Right Ventricle	heart
15	chr8:19523200-19528200	Weak transcription	Right Atrium	heart
16	chr8:19523200-19533200	Weak transcription	Pancreas	Pancrea
17	chr8:19523200-19534600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr8:19523400-19529600	Weak transcription	Fetal Brain Female	brain
19	chr8:19523600-19538600	Weak transcription	Brain Anterior Caudate	brain
20	chr8:19523800-19529600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr8:19523800-19540200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr8:19524000-19528600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr8:19524000-19528800	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr8:19524200-19527600	Weak transcription	Fetal Brain Male	brain
25	chr8:19524200-19535200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr8:19524200-19539000	Weak transcription	Ovary	ovary
27	chr8:19525000-19533400	Weak transcription	Placenta	Placenta
28	chr8:19525200-19532800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr8:19525200-19533400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr8:19525400-19538800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr8:19525600-19530400	Weak transcription	Primary T cells from cord blood	blood
32	chr8:19525600-19530600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr8:19525800-19529000	Enhancers	Primary B cells from peripheral blood	blood
34	chr8:19526000-19528800	Enhancers	Left Ventricle	heart
35	chr8:19526200-19529000	Enhancers	A549	lung
36	chr8:19526400-19527600	Weak transcription	Fetal Heart	heart
37	chr8:19526400-19528400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr8:19526400-19528400	Weak transcription	Spleen	Spleen
39	chr8:19526800-19528000	Enhancers	Hela-S3	cervix
40	chr8:19527200-19527800	Enhancers	Aorta	Aorta
41	chr8:19527200-19527800	Enhancers	Brain Cingulate Gyrus	brain
42	chr8:19527400-19527800	Flanking Active TSS	GM12878-XiMat	blood
43	chr8:19527400-19528400	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr8:19527400-19529200	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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