Variant report

Variant	rs6846822
Chromosome Location	chr4:87816003-87816004
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	STAT3	chr4:87815561-87816046	MCF10A-Er-Src	breast:	n/a	chr4:87815774-87815782
2	GATA2	chr4:87815720-87816072	HUVEC	blood vessel:	n/a	chr4:87815854-87815868 chr4:87815797-87815807
3	FOS	chr4:87815621-87816009	MCF10A-Er-Src	breast:	n/a	chr4:87815806-87815817
4	POLR2A	chr4:87815538-87816112	MCF10A-Er-Src	breast:	n/a	n/a
5	JUN	chr4:87815631-87816003	HUVEC	blood vessel:	n/a	n/a
6	YY1	chr4:87815759-87816126	K562	blood:	n/a	n/a
7	FOS	chr4:87815572-87816085	HUVEC	blood vessel:	n/a	chr4:87815806-87815817
8	STAT3	chr4:87815560-87816047	MCF10A-Er-Src	breast:	n/a	chr4:87815774-87815782
9	JUND	chr4:87815668-87816012	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87813108..87815411-chr4:87815518..87817081,3	K562	blood:
2	chr4:87416805..87418843-chr4:87815414..87817028,2	MCF-7	breast:

Variant related genes	Relation type
C4orf36	TF binding region
ENSG00000163633	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10011798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10015121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10015477	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10015508	0.86[YRI][hapmap]
rs10021020	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10021790	0.85[ASN][1000 genomes]
rs10034336	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1010902	0.97[ASN][1000 genomes]
rs1010903	0.97[ASN][1000 genomes]
rs11097123	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11097125	1.00[EUR][1000 genomes]
rs12503045	1.00[EUR][1000 genomes]
rs12507165	1.00[EUR][1000 genomes]
rs12641570	1.00[EUR][1000 genomes]
rs13115795	0.96[ASN][1000 genomes]
rs13120981	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13137483	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1374935	0.98[EUR][1000 genomes]
rs17012132	0.86[ASN][1000 genomes]
rs17751557	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs1868244	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1985944	0.97[ASN][1000 genomes]
rs2121871	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2594274	0.98[EUR][1000 genomes]
rs2594283	0.94[EUR][1000 genomes]
rs2705629	0.99[EUR][1000 genomes]
rs28446826	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28641910	1.00[ASN][1000 genomes]
rs28650493	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28716151	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2904148	0.94[EUR][1000 genomes]
rs2904150	0.98[EUR][1000 genomes]
rs35428486	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4235082	0.99[EUR][1000 genomes]
rs4693154	0.89[JPT][hapmap]
rs55698195	0.88[ASN][1000 genomes]
rs55889191	0.95[EUR][1000 genomes]
rs56062410	0.91[EUR][1000 genomes]
rs56201068	0.92[ASN][1000 genomes]
rs6531935	0.82[TSI][hapmap]
rs67758970	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6823051	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6843070	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs72667703	0.97[ASN][1000 genomes]
rs72667705	0.96[ASN][1000 genomes]
rs727143	0.86[YRI][hapmap]

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
rs6846822	PTPN13	cis	cerebellum	SCAN
rs6846822	PTPN13	cis	parietal	SCAN
rs6846822	AFF1	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87814000-87817400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr4:87814000-87825000	Weak transcription	Right Atrium	heart
3	chr4:87814000-87825200	Weak transcription	Left Ventricle	heart
4	chr4:87814200-87817200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr4:87814200-87824800	Weak transcription	Adipose Nuclei	Adipose
6	chr4:87814200-87825000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:87814200-87825200	Weak transcription	Right Ventricle	heart
8	chr4:87814200-87825200	Weak transcription	A549	lung
9	chr4:87814200-87829400	Weak transcription	K562	blood
10	chr4:87814400-87825000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:87814400-87825200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:87814400-87825200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr4:87814600-87821600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:87814600-87821600	Weak transcription	Placenta	Placenta
15	chr4:87814600-87825200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:87814600-87830000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:87814800-87818000	Enhancers	NHEK	skin
18	chr4:87815400-87816200	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr4:87815400-87816600	Enhancers	HUVEC	blood vessel
20	chr4:87815600-87816200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:87815600-87816200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:87815600-87816200	Enhancers	HMEC	breast
23	chr4:87815800-87816200	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr4:87816000-87816200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:87816000-87816200	Enhancers	Esophagus	oesophagus
26	chr4:87816000-87816200	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr4:87816000-87818800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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