Variant report

Variant	rs2250616
Chromosome Location	chr4:110836564-110836565
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: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10002971	0.85[EUR][1000 genomes]
rs10011112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10014383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10017261	0.90[EUR][1000 genomes]
rs10023272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10029105	0.95[EUR][1000 genomes]
rs10029654	0.96[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs10213531	0.94[EUR][1000 genomes]
rs1024600	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10470911	1.00[CEU][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs10488881	1.00[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs11098056	0.91[EUR][1000 genomes]
rs11568903	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11568905	0.80[EUR][1000 genomes]
rs11568950	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11568972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11568994	0.87[CEU][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs17238095	1.00[ASN][1000 genomes]
rs17253063	0.85[EUR][1000 genomes]
rs17316633	1.00[ASN][1000 genomes]
rs2024114	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2067004	0.96[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs2190909	0.93[EUR][1000 genomes]
rs2237041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237045	0.94[EUR][1000 genomes]
rs2282785	0.95[EUR][1000 genomes]
rs2298977	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2347136	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28437404	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535066	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28540029	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28564978	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28629923	0.95[EUR][1000 genomes]
rs28672708	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28734982	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764861	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs3775967	0.97[EUR][1000 genomes]
rs3796945	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796946	0.95[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs3822288	0.96[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs4279279	0.92[EUR][1000 genomes]
rs4698755	0.96[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs4698756	0.88[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs4698800	0.96[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs4698801	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs62327602	1.00[ASN][1000 genomes]
rs62327604	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6533481	0.95[EUR][1000 genomes]
rs6837717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6850557	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs7655579	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs7668520	0.96[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs7680062	0.81[EUR][1000 genomes]
rs881878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307347	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9991904	0.81[JPT][hapmap];0.83[MEX][hapmap]
rs9992755	0.96[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2250616	GAR1	cis	cerebellum	SCAN

Chromatin state (count:39 , 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	chr4:110833800-110837600	Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr4:110834000-110837200	Active TSS	Pancreas	Pancrea
4	chr4:110834000-110837400	Active TSS	Psoas Muscle	Psoas
5	chr4:110834000-110838400	Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr4:110834200-110836600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:110834200-110837000	Active TSS	Fetal Muscle Trunk	muscle
8	chr4:110834200-110837200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:110834400-110844800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:110834600-110836600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:110834600-110837200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:110834600-110841800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:110834800-110837400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr4:110835200-110842200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:110835400-110837400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:110835600-110836600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:110835600-110836800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:110835600-110837000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:110835600-110837000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr4:110835800-110836600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr4:110835800-110836600	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr4:110835800-110836600	Enhancers	Right Ventricle	heart
23	chr4:110835800-110837600	Enhancers	Fetal Heart	heart
24	chr4:110836000-110836800	Enhancers	Colonic Mucosa	Colon
25	chr4:110836000-110837200	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr4:110836000-110837400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr4:110836200-110836800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr4:110836200-110837400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr4:110836200-110837800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:110836200-110841600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr4:110836400-110836600	Active TSS	Left Ventricle	heart
32	chr4:110836400-110836600	Enhancers	A549	lung
33	chr4:110836400-110836600	Flanking Active TSS	HSMMtube	muscle
34	chr4:110836400-110836600	Enhancers	K562	blood
35	chr4:110836400-110836800	Flanking Active TSS	Fetal Intestine Large	intestine
36	chr4:110836400-110836800	Flanking Active TSS	Fetal Intestine Small	intestine
37	chr4:110836400-110837400	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr4:110836400-110837800	Enhancers	Primary hematopoietic stem cells	blood
39	chr4:110836400-110840000	Weak transcription	Placenta Amnion	Placenta Amnion

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