Variant report

Variant	rs1022197
Chromosome Location	chr15:77290041-77290042
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1022198	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905311	0.91[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12908255	0.91[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1567670	0.82[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16968623	0.95[JPT][hapmap]
rs1877435	0.82[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1877436	0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2254441	1.00[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2458246	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2458254	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2469200	0.82[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2469202	0.82[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2469203	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2469227	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2469232	0.86[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7173067	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs7175783	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8030698	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv2758388	chr15:77170550-77373448	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS 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	18 gene(s)	inside rSNPs	diseases
5	esv2760041	chr15:77170550-77373448	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv833058	chr15:77235895-77393640	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv517068	chr15:77254544-77381222	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv1808532	chr15:77257714-77332539	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1043017	chr15:77266776-77309938	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1035874	chr15:77266776-77328742	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv1822592	chr15:77283956-77332539	Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv570111	chr15:77286693-77332606	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1022197	TSPAN3	cis	cerebellum	SCAN
rs1022197	Contig57330_RC	cis	multi-tissue	Pritchard
rs1022197	CSK	cis	parietal	SCAN
rs1022197	SGK269	cis	Liver	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77283000-77291000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr15:77287200-77290200	Flanking Active TSS	GM12878-XiMat	blood
3	chr15:77287600-77290800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:77288000-77290200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:77288000-77290200	Enhancers	HMEC	breast
6	chr15:77288000-77290400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr15:77288000-77290600	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr15:77288000-77290800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr15:77288200-77293600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:77288800-77290200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr15:77289000-77290200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:77289000-77291000	Weak transcription	Brain Angular Gyrus	brain
13	chr15:77289200-77290800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:77289200-77290800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:77289200-77311200	Weak transcription	Aorta	Aorta
16	chr15:77289400-77290800	Weak transcription	HSMMtube	muscle
17	chr15:77289400-77291000	Weak transcription	Brain Hippocampus Middle	brain
18	chr15:77289400-77292800	Enhancers	Fetal Thymus	thymus
19	chr15:77289400-77299000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr15:77289400-77302200	Weak transcription	Pancreas	Pancrea
21	chr15:77289400-77305200	Weak transcription	Esophagus	oesophagus
22	chr15:77289400-77310000	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:77289600-77290200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr15:77289600-77290200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:77289600-77290800	Enhancers	NHEK	skin
26	chr15:77289600-77291000	Weak transcription	Placenta	Placenta
27	chr15:77289600-77291200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
28	chr15:77289600-77291400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr15:77289600-77293400	Weak transcription	Spleen	Spleen
30	chr15:77289600-77294400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:77289600-77294400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr15:77289600-77294800	Weak transcription	HSMM	muscle
33	chr15:77289600-77295000	Weak transcription	Colonic Mucosa	Colon
34	chr15:77289600-77301600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr15:77289800-77290200	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:77289800-77290200	Enhancers	Duodenum Mucosa	Duodenum
37	chr15:77289800-77290800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr15:77289800-77291000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr15:77289800-77291000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr15:77289800-77291000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr15:77289800-77294400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:77289800-77294400	Weak transcription	Thymus	Thymus
43	chr15:77289800-77294600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr15:77289800-77296200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr15:77289800-77297400	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr15:77290000-77290200	Enhancers	Primary hematopoietic stem cells	blood
47	chr15:77290000-77290600	Genic enhancers	Primary B cells from cord blood	blood
48	chr15:77290000-77290600	Enhancers	Primary T cells fromperipheralblood	blood
49	chr15:77290000-77290600	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr15:77290000-77290800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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