Variant report

Variant	rs3099418
Chromosome Location	chr8:95554429-95554430
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:95554407-95554542	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:95553642..95556255-chr8:95557800..95559824,2	K562	blood:
2	chr8:95546560..95549138-chr8:95553073..95555692,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212997	TF binding region
ENSG00000212997	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11784188	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11786245	0.88[ASN][1000 genomes]
rs11992717	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17716313	0.83[CEU][hapmap]
rs1866844	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.98[ASN][1000 genomes]
rs1978556	0.87[ASN][1000 genomes]
rs2304765	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2890827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3096604	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs3098705	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3098711	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3098713	0.82[YRI][hapmap]
rs3098714	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3098717	0.82[YRI][hapmap]
rs3098721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3098722	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3098723	0.82[YRI][hapmap]
rs3098724	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099405	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3099408	0.82[YRI][hapmap]
rs3099414	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3099419	0.82[YRI][hapmap]
rs3099420	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3099421	0.82[YRI][hapmap]
rs3099422	0.87[ASN][1000 genomes]
rs3099425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3102852	0.87[ASN][1000 genomes]
rs3102854	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3102856	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3102857	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3102858	0.82[YRI][hapmap]
rs3102860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3102865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3102866	0.82[YRI][hapmap]
rs3102870	0.82[YRI][hapmap]
rs3133598	0.82[YRI][hapmap]
rs3133600	0.88[ASN][1000 genomes]
rs3133636	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3133639	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3133644	0.89[YRI][hapmap]
rs3133646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3133647	0.82[YRI][hapmap]
rs3133659	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv611750	chr8:95519205-95574634	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3099418	TSPYL5	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95497200-95564200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr8:95516800-95554600	Strong transcription	Fetal Thymus	thymus
3	chr8:95520400-95555200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr8:95532800-95558800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr8:95535400-95556000	Weak transcription	Fetal Heart	heart
6	chr8:95535800-95555600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr8:95536000-95555600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr8:95536600-95557000	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr8:95536800-95556600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr8:95537000-95557400	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr8:95537000-95558600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr8:95537200-95554800	Strong transcription	Fetal Intestine Large	intestine
13	chr8:95541600-95563600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr8:95541600-95563800	Weak transcription	Stomach Mucosa	stomach
15	chr8:95543200-95563200	Weak transcription	Fetal Brain Male	brain
16	chr8:95543200-95564800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr8:95543200-95564800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr8:95543600-95558000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr8:95543600-95564000	Weak transcription	HSMMtube	muscle
20	chr8:95544400-95558000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr8:95545200-95564000	Weak transcription	Psoas Muscle	Psoas
22	chr8:95546200-95555200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr8:95546200-95564800	Weak transcription	Esophagus	oesophagus
24	chr8:95546400-95564000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr8:95546400-95564000	Weak transcription	Aorta	Aorta
26	chr8:95546600-95563600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr8:95546800-95558400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr8:95546800-95563600	Weak transcription	Brain Angular Gyrus	brain
29	chr8:95547000-95563000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr8:95547000-95564000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr8:95547000-95565000	Weak transcription	Pancreas	Pancrea
32	chr8:95547200-95563200	Weak transcription	Gastric	stomach
33	chr8:95547400-95563200	Weak transcription	Brain Substantia Nigra	brain
34	chr8:95547400-95563600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr8:95548000-95563600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr8:95548400-95563800	Weak transcription	Brain Hippocampus Middle	brain
37	chr8:95548400-95563800	Weak transcription	Small Intestine	intestine
38	chr8:95548800-95564000	Weak transcription	Colonic Mucosa	Colon
39	chr8:95549000-95558800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr8:95549000-95563000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr8:95549000-95563800	Weak transcription	HUVEC	blood vessel
42	chr8:95549000-95564000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr8:95549000-95564000	Weak transcription	Brain Germinal Matrix	brain
44	chr8:95549400-95555400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr8:95549400-95561800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr8:95549400-95563200	Weak transcription	Ovary	ovary
47	chr8:95549400-95563400	Weak transcription	NHDF-Ad	bronchial
48	chr8:95549400-95564000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr8:95549600-95563800	Weak transcription	Brain Anterior Caudate	brain
50	chr8:95550000-95563600	Weak transcription	NH-A	brain

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