Variant report

Variant	rs4235078
Chromosome Location	chr4:87029318-87029319
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	PBX3	chr4:87029230-87029812	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr4:87029279-87029711	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr4:87029300-87029883	SK-N-SH	brain:	n/a	n/a
4	TEAD4	chr4:87029258-87029736	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr4:87029224-87029690	SK-N-SH	brain:	n/a	n/a
6	JUND	chr4:87029126-87029851	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr4:87029143-87029901	SK-N-SH	brain:	n/a	n/a
8	PBX3	chr4:87029301-87029688	SK-N-SH	brain:	n/a	n/a
9	JUND	chr4:87029212-87029800	SK-N-SH	brain:	n/a	n/a
10	EP300	chr4:87029309-87029842	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
MAPK10	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10001480	0.88[JPT][hapmap]
rs10212744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10776485	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505595	0.82[JPT][hapmap]
rs12647176	0.88[JPT][hapmap]
rs12647506	0.88[JPT][hapmap]
rs2575675	0.82[JPT][hapmap]
rs28529458	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3775182	0.82[JPT][hapmap]
rs4289439	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4334746	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];0.95[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4352468	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4403040	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4407492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4546235	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4560400	0.88[JPT][hapmap]
rs4693136	0.88[JPT][hapmap]
rs4693756	0.81[JPT][hapmap]
rs4693757	0.88[JPT][hapmap]
rs6854208	0.88[JPT][hapmap]
rs7699978	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009622	chr4:86893536-87119153	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1003585	chr4:86957967-87250436	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2754254	chr4:86979147-87108510	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv879521	chr4:86979927-87165758	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1005338	chr4:87023398-87108555	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4235078	CDS1	cis	parietal	SCAN
rs4235078	PTPN13	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87005000-87050400	Weak transcription	Brain Angular Gyrus	brain
2	chr4:87005600-87031200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr4:87005600-87035200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:87010800-87035800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:87011400-87035600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:87023400-87038800	Weak transcription	Brain Anterior Caudate	brain
7	chr4:87026000-87029800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr4:87026800-87032600	Weak transcription	Fetal Brain Male	brain
9	chr4:87027400-87029400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:87027800-87029800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:87027800-87029800	Enhancers	Osteobl	bone
12	chr4:87027800-87030000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:87028200-87029600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr4:87028200-87030000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr4:87028600-87030000	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr4:87029000-87029800	Enhancers	NHDF-Ad	bronchial
17	chr4:87029000-87030000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr4:87029000-87032000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:87029200-87029800	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr4:87029200-87029800	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr4:87029200-87030000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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