Variant report

Variant	rs2469202
Chromosome Location	chr15:77282884-77282885
allele	A/G
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	ZNF143	chr15:77282763-77283031	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77280561..77283110-chr15:77283637..77286723,3	MCF-7	breast:

Variant related genes	Relation type
PSTPIP1	TF binding region
ENSG00000140368	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1022197	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]
rs1022198	0.82[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12905311	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs12908255	0.82[JPT][hapmap]
rs1567670	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16968623	0.82[JPT][hapmap]
rs1877435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1877436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2254441	0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2458246	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2458254	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2469200	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2469203	0.95[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2469227	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2469232	0.93[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7173067	0.82[JPT][hapmap]
rs7175783	0.82[AMR][1000 genomes]
rs8030698	0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.81[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2469202	TSPAN3	cis	cerebellum	SCAN
rs2469202	CSK	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77274000-77287200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr15:77281200-77286400	Weak transcription	Colonic Mucosa	Colon
3	chr15:77281200-77286400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr15:77281400-77285800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr15:77281400-77286000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:77281400-77286400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr15:77281600-77284600	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr15:77281600-77285600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:77281600-77285600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr15:77281600-77285600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr15:77281600-77285600	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr15:77281600-77285600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr15:77281600-77285800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr15:77281600-77285800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr15:77281600-77286000	Weak transcription	Primary T cells from cord blood	blood
16	chr15:77281600-77286000	Weak transcription	Lung	lung
17	chr15:77281600-77286200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr15:77281600-77286400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:77281600-77287800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:77281600-77289000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:77281800-77283000	Weak transcription	Pancreas	Pancrea
22	chr15:77281800-77283200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:77281800-77283200	Weak transcription	Primary B cells from cord blood	blood
24	chr15:77281800-77283200	Weak transcription	Right Atrium	heart
25	chr15:77281800-77283400	Enhancers	GM12878-XiMat	blood
26	chr15:77281800-77284800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr15:77281800-77284800	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:77281800-77285600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr15:77281800-77285600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:77281800-77285800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr15:77281800-77286000	Weak transcription	Primary B cells from peripheral blood	blood
32	chr15:77281800-77286400	Weak transcription	Fetal Thymus	thymus
33	chr15:77281800-77287400	Weak transcription	Brain Anterior Caudate	brain
34	chr15:77281800-77287800	Weak transcription	Brain Angular Gyrus	brain
35	chr15:77281800-77288000	Weak transcription	Liver	Liver
36	chr15:77281800-77288600	Weak transcription	Left Ventricle	heart
37	chr15:77281800-77289000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr15:77282000-77283000	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr15:77282000-77283400	Weak transcription	Adipose Nuclei	Adipose
40	chr15:77282000-77284200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr15:77282000-77284200	Weak transcription	Fetal Muscle Leg	muscle
42	chr15:77282000-77284600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr15:77282000-77284600	Weak transcription	Spleen	Spleen
44	chr15:77282000-77285400	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr15:77282000-77285600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr15:77282000-77287200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr15:77282000-77287200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr15:77282000-77287400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr15:77282000-77287400	Weak transcription	Right Ventricle	heart
50	chr15:77282000-77287600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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