Variant report

Variant	rs3102854
Chromosome Location	chr8:95497989-95497990
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11784188	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11992717	0.83[ASN][1000 genomes]
rs1866844	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2304765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2890827	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3096604	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs3098705	0.86[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3098711	0.94[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3098714	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3098721	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3098722	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3098724	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3099405	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099411	0.88[YRI][hapmap]
rs3099414	0.87[ASN][1000 genomes]
rs3099418	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3099420	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3099425	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3102844	0.88[YRI][hapmap]
rs3102856	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3102857	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3102860	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3102865	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3133636	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3133639	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3133646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3133659	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]

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	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv532338	chr8:95296118-95971825	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv429928	chr8:95488800-95672033	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3102854	TSPYL5	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95487800-95500000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr8:95487800-95500200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr8:95488000-95498800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr8:95488000-95499000	Weak transcription	NHDF-Ad	bronchial
5	chr8:95488000-95499200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr8:95488000-95499200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr8:95488000-95499400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr8:95488000-95499400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr8:95488000-95499400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr8:95488000-95499400	Weak transcription	Adipose Nuclei	Adipose
11	chr8:95488000-95499400	Weak transcription	Brain Germinal Matrix	brain
12	chr8:95488000-95499400	Weak transcription	Brain Hippocampus Middle	brain
13	chr8:95488000-95499400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr8:95488000-95499400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr8:95488000-95499400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr8:95488000-95499600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr8:95488000-95499600	Weak transcription	Liver	Liver
18	chr8:95488000-95499600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr8:95488000-95499600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr8:95488000-95499600	Weak transcription	Osteobl	bone
21	chr8:95488000-95499800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr8:95488000-95499800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr8:95488000-95500000	Weak transcription	GM12878-XiMat	blood
24	chr8:95488000-95500200	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr8:95488000-95500200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr8:95488000-95500400	Weak transcription	Primary B cells from cord blood	blood
27	chr8:95488000-95500400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr8:95488000-95500400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr8:95488000-95500400	Weak transcription	HMEC	breast
30	chr8:95488000-95500400	Weak transcription	HUVEC	blood vessel
31	chr8:95488000-95501800	Weak transcription	Colon Smooth Muscle	Colon
32	chr8:95488000-95502200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr8:95488000-95503600	Weak transcription	NHEK	skin
34	chr8:95488200-95499200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr8:95488200-95499400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr8:95488200-95500200	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr8:95488200-95501000	Weak transcription	Hela-S3	cervix
38	chr8:95488200-95507800	Weak transcription	NHLF	lung
39	chr8:95491200-95499400	Weak transcription	Placenta	Placenta
40	chr8:95491200-95499400	Weak transcription	HSMM	muscle
41	chr8:95491600-95499200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr8:95492000-95500400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr8:95492200-95499200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr8:95492200-95503000	Weak transcription	HepG2	liver
45	chr8:95492600-95499600	Weak transcription	Brain Substantia Nigra	brain
46	chr8:95493000-95549200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr8:95493200-95500200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr8:95493400-95499400	Weak transcription	Left Ventricle	heart
49	chr8:95493400-95503600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr8:95494000-95499400	Weak transcription	Placenta Amnion	Placenta Amnion

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