Variant report

Variant	rs2298978
Chromosome Location	chr4:110837667-110837668
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:110831685..110835620-chr4:110836473..110840110,4	K562	blood:

Variant related genes	Relation type
ENSG00000138798	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10014805	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10015002	0.89[EUR][1000 genomes]
rs10017564	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10021157	0.93[ASW][hapmap];0.89[CEU][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10025078	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10025276	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11568904	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12503113	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12506489	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506702	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12510173	0.96[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12640600	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1860129	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2074390	0.83[MEX][hapmap]
rs2190907	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2237040	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2237049	0.87[MEX][hapmap]
rs2237051	0.87[MEX][hapmap]
rs2282784	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2298979	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2298983	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2298989	0.81[CEU][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs2298991	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs2298992	0.88[EUR][1000 genomes]
rs2298993	0.85[EUR][1000 genomes]
rs2347137	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2881559	0.96[CEU][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3796944	1.00[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3796948	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4444903	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6533482	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6533483	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6824594	0.87[MEX][hapmap]
rs6855847	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs882405	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs882471	0.82[MEX][hapmap]
rs929446	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9994491	0.89[EUR][1000 genomes]
rs9994509	0.86[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	nsv530156	chr4:110721397-110911297	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	esv1806286	chr4:110837287-110845707	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv1811274	chr4:110837287-110845707	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv1814770	chr4:110837287-110845707	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2298978	GAR1	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110833600-110838000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:110834000-110838400	Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr4:110834400-110844800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:110834600-110841800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:110835200-110842200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr4:110836200-110837800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:110836200-110841600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr4:110836400-110837800	Enhancers	Primary hematopoietic stem cells	blood
9	chr4:110836400-110840000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr4:110836600-110839600	Weak transcription	Right Ventricle	heart
11	chr4:110836600-110842000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:110836800-110842400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr4:110836800-110842600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr4:110836800-110849400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr4:110837000-110837800	Enhancers	Duodenum Mucosa	Duodenum
16	chr4:110837000-110840400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:110837000-110842000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:110837200-110837800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:110837200-110837800	Flanking Active TSS	Fetal Intestine Large	intestine
20	chr4:110837200-110838000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:110837200-110839400	Weak transcription	Pancreas	Pancrea
22	chr4:110837200-110842000	Weak transcription	HSMMtube	muscle
23	chr4:110837400-110837800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr4:110837400-110837800	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr4:110837400-110837800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:110837400-110839600	Weak transcription	Psoas Muscle	Psoas
27	chr4:110837400-110842000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:110837600-110838000	Enhancers	Fetal Intestine Small	intestine
29	chr4:110837600-110842600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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