Variant report

Variant	rs2798298
Chromosome Location	chr4:3036602-3036603
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	chr4:3027654..3029286-chr4:3034423..3037421,2	K562	blood:
2	chr4:3022215..3024968-chr4:3035752..3037609,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125388	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1008210	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1010290	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1313768	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1313771	0.90[ASN][1000 genomes]
rs1557213	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1801058	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071688	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071689	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2157097	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2187694	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2187695	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2211474	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2471347	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2798286	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2798303	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2798304	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2857839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857840	1.00[ASN][1000 genomes]
rs2857841	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857849	0.92[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2857852	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs732859	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	nsv1013440	chr4:2993130-3053503	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2798298	GRK4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3005800-3038600	Weak transcription	Right Ventricle	heart
2	chr4:3011800-3039600	Weak transcription	Right Atrium	heart
3	chr4:3019200-3039000	Weak transcription	Left Ventricle	heart
4	chr4:3021200-3043000	Weak transcription	Brain Germinal Matrix	brain
5	chr4:3024600-3038800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:3024800-3038800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr4:3025200-3038800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr4:3025200-3039000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:3025200-3039000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr4:3025200-3039000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:3025200-3043400	Weak transcription	Aorta	Aorta
12	chr4:3025400-3039000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr4:3025600-3039000	Weak transcription	Fetal Lung	lung
14	chr4:3025600-3042800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:3025600-3042800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:3028000-3038400	Weak transcription	Fetal Intestine Small	intestine
17	chr4:3029600-3039000	Weak transcription	Brain Anterior Caudate	brain
18	chr4:3032400-3042400	Weak transcription	Fetal Brain Female	brain
19	chr4:3033000-3037800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:3033400-3037800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:3033600-3037800	Weak transcription	Spleen	Spleen
22	chr4:3033600-3039000	Weak transcription	Pancreas	Pancrea
23	chr4:3033800-3038600	Weak transcription	Gastric	stomach
24	chr4:3035200-3038000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:3035400-3038600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:3036000-3037800	Weak transcription	Fetal Muscle Leg	muscle
27	chr4:3036200-3037600	Weak transcription	HSMMtube	muscle

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