Variant report

Variant	rs2469203
Chromosome Location	chr15:77296134-77296135
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1022197	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]
rs1022198	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12905311	0.95[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12908255	0.95[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1567670	0.98[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16968623	0.95[JPT][hapmap]
rs1877435	0.86[JPT][hapmap];0.80[AMR][1000 genomes]
rs1877436	0.86[JPT][hapmap]
rs2254441	0.93[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2458246	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2458254	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2469200	0.95[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2469202	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	0.86[JPT][hapmap]
rs2469232	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173067	0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7175783	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8030698	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
13	nsv1048833	chr15:77294593-77339260	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2469203	TSPAN3	cis	cerebellum	SCAN
rs2469203	CSK	cis	parietal	SCAN
rs2469203	PSTPIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77289200-77311200	Weak transcription	Aorta	Aorta
2	chr15:77289400-77299000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr15:77289400-77302200	Weak transcription	Pancreas	Pancrea
4	chr15:77289400-77305200	Weak transcription	Esophagus	oesophagus
5	chr15:77289400-77310000	Weak transcription	Colon Smooth Muscle	Colon
6	chr15:77289600-77301600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:77289800-77296200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr15:77289800-77297400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr15:77290200-77306000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:77291200-77299600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr15:77293800-77296800	Enhancers	Duodenum Mucosa	Duodenum
12	chr15:77293800-77296800	Enhancers	Fetal Thymus	thymus
13	chr15:77293800-77297000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:77294000-77296800	Enhancers	Primary hematopoietic stem cells	blood
15	chr15:77294200-77297000	Enhancers	Spleen	Spleen
16	chr15:77294200-77297400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr15:77294200-77298400	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr15:77294400-77296200	Enhancers	Thymus	Thymus
19	chr15:77294600-77296200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:77294600-77297400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr15:77294800-77296200	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr15:77294800-77296400	Flanking Active TSS	GM12878-XiMat	blood
23	chr15:77295000-77296200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr15:77295000-77296200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr15:77295000-77296600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr15:77295000-77298400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr15:77295200-77296400	Weak transcription	Placenta	Placenta
28	chr15:77295400-77296600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr15:77295400-77296800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr15:77295400-77297800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:77295400-77298000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr15:77295400-77302400	Weak transcription	Colonic Mucosa	Colon
33	chr15:77295600-77296600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:77295600-77296600	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr15:77295600-77297000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr15:77295600-77297400	Enhancers	Primary B cells from cord blood	blood
37	chr15:77295600-77305200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr15:77295800-77296200	Weak transcription	Adipose Nuclei	Adipose
39	chr15:77295800-77296400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr15:77295800-77299600	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr15:77295800-77305000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr15:77296000-77296600	Enhancers	Liver	Liver
43	chr15:77296000-77297000	Genic enhancers	Primary B cells from peripheral blood	blood

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