Variant report

Variant	rs10109456
Chromosome Location	chr8:19565942-19565943
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10086135	1.00[CEU][hapmap]
rs10091557	1.00[EUR][1000 genomes]
rs17408029	1.00[MEX][hapmap]
rs55763426	1.00[EUR][1000 genomes]
rs61196448	0.90[EUR][1000 genomes]
rs73202505	1.00[EUR][1000 genomes]
rs73202509	1.00[EUR][1000 genomes]
rs73202513	0.90[EUR][1000 genomes]
rs73216641	0.90[EUR][1000 genomes]
rs73216645	0.90[EUR][1000 genomes]
rs73216651	0.90[EUR][1000 genomes]
rs73216656	0.90[EUR][1000 genomes]
rs73218618	0.90[EUR][1000 genomes]
rs73218623	0.90[EUR][1000 genomes]
rs73218625	1.00[EUR][1000 genomes]
rs73218626	1.00[EUR][1000 genomes]
rs73218631	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73218634	1.00[EUR][1000 genomes]
rs73218635	0.90[EUR][1000 genomes]
rs73218638	1.00[EUR][1000 genomes]
rs7828018	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
6	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
7	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
8	nsv1021225	chr8:19554860-19586580	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv610759	chr8:19561997-20068842	Enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10109456	CCL4	trans	brain	seeQTL
rs10109456	PTGS2	trans	brain	seeQTL
rs10109456	FOSB	trans	brain	seeQTL
rs10109456	EGR4	trans	brain	seeQTL
rs10109456	EGR2	trans	brain	seeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19541000-19567400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr8:19555000-19573200	Weak transcription	Pancreas	Pancrea
3	chr8:19555200-19566000	Weak transcription	Lung	lung
4	chr8:19555200-19567200	Weak transcription	Fetal Brain Male	brain
5	chr8:19555200-19573600	Weak transcription	Fetal Stomach	stomach
6	chr8:19555400-19566000	Weak transcription	Right Ventricle	heart
7	chr8:19557200-19566200	Weak transcription	Hela-S3	cervix
8	chr8:19558600-19570800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr8:19558600-19573400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr8:19559200-19571200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr8:19559200-19573400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr8:19559200-19573600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr8:19562800-19567400	Enhancers	Primary B cells from cord blood	blood
14	chr8:19563000-19569400	Enhancers	Primary B cells from peripheral blood	blood
15	chr8:19563200-19578200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr8:19564000-19567800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr8:19564200-19567000	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr8:19564200-19567000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr8:19564200-19567200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr8:19564200-19570800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr8:19564200-19571000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr8:19564600-19566200	Weak transcription	Left Ventricle	heart
23	chr8:19564600-19566600	Weak transcription	Right Atrium	heart
24	chr8:19564600-19567200	Weak transcription	Brain Anterior Caudate	brain
25	chr8:19564600-19570600	Weak transcription	Fetal Muscle Leg	muscle
26	chr8:19564600-19571000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr8:19564800-19567600	Weak transcription	Brain Hippocampus Middle	brain
28	chr8:19564800-19570600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr8:19564800-19571000	Weak transcription	Aorta	Aorta
30	chr8:19565000-19566000	Weak transcription	A549	lung
31	chr8:19565600-19566200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr8:19565600-19566400	Enhancers	GM12878-XiMat	blood
33	chr8:19565600-19566800	Enhancers	HUVEC	blood vessel
34	chr8:19565600-19567400	Enhancers	Placenta	Placenta
35	chr8:19565800-19566200	Genic enhancers	Primary T cells from cord blood	blood
36	chr8:19565800-19566400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr8:19565800-19568200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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