Variant report

Variant	rs1868244
Chromosome Location	chr4:87815387-87815388
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10011798	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs10015121	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs10021020	0.98[EUR][1000 genomes]
rs10034336	0.99[EUR][1000 genomes]
rs11097123	0.89[EUR][1000 genomes]
rs11097125	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12503045	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507165	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12641570	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13120981	0.98[EUR][1000 genomes]
rs1374935	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2012345	0.97[ASN][1000 genomes]
rs2121871	0.96[CEU][hapmap];0.85[JPT][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs2594274	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2594283	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2705629	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28446826	0.87[EUR][1000 genomes]
rs2904148	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2904150	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35428486	0.97[EUR][1000 genomes]
rs4235082	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55889191	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56062410	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6531935	0.82[TSI][hapmap]
rs67758970	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823051	0.99[EUR][1000 genomes]
rs6843070	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6846822	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][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	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv508297	chr4:87778783-87868508	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1868244	PTPN13	cis	parietal	SCAN
rs1868244	AFF1	cis	cerebellum	SCAN
rs1868244	PTPN13	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87814000-87815600	Weak transcription	Hela-S3	cervix
2	chr4:87814000-87817400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:87814000-87825000	Weak transcription	Right Atrium	heart
4	chr4:87814000-87825200	Weak transcription	Left Ventricle	heart
5	chr4:87814200-87815400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:87814200-87815600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr4:87814200-87817200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr4:87814200-87824800	Weak transcription	Adipose Nuclei	Adipose
9	chr4:87814200-87825000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:87814200-87825200	Weak transcription	Right Ventricle	heart
11	chr4:87814200-87825200	Weak transcription	A549	lung
12	chr4:87814200-87829400	Weak transcription	K562	blood
13	chr4:87814400-87815400	Weak transcription	HUVEC	blood vessel
14	chr4:87814400-87815400	Weak transcription	NH-A	brain
15	chr4:87814400-87815600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:87814400-87815600	Weak transcription	HMEC	breast
17	chr4:87814400-87815600	Weak transcription	NHDF-Ad	bronchial
18	chr4:87814400-87815600	Weak transcription	Osteobl	bone
19	chr4:87814400-87816000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:87814400-87825000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr4:87814400-87825200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:87814400-87825200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr4:87814600-87815600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:87814600-87815600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:87814600-87815600	Weak transcription	NHLF	lung
26	chr4:87814600-87815800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:87814600-87816000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:87814600-87821600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:87814600-87821600	Weak transcription	Placenta	Placenta
30	chr4:87814600-87825200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:87814600-87830000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:87814800-87815800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:87814800-87818000	Enhancers	NHEK	skin
34	chr4:87815000-87815800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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