Variant report

Variant	rs2471350
Chromosome Location	chr4:3014319-3014320
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3014192..3017069-chr4:3021177..3023631,3	MCF-7	breast:
2	chr4:2963576..2965499-chr4:3012277..3014401,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125388	Chromatin interaction
ENSG00000087269	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1018789	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1024323	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1054090	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12500735	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504022	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13120295	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13143902	0.82[ASN][1000 genomes]
rs13146104	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419044	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1475975	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1475976	0.80[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap]
rs1475977	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1891710	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2032463	0.85[CHB][hapmap]
rs2185886	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2256086	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2342295	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2471321	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2471326	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2471327	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2471328	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2488804	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2488805	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2488806	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2488809	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2488815	1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2515932	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2515933	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2515935	0.83[CEU][hapmap]
rs2515936	0.83[CEU][hapmap]
rs2515943	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2960295	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2960308	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6834738	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729826	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7658707	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7679865	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv1008436	chr4:2947160-3031195	Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv536998	chr4:2947160-3031195	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv593438	chr4:2948456-3030097	Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1008527	chr4:2957814-3019042	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv878453	chr4:2963222-3021383	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1008781	chr4:2964080-3019042	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv870141	chr4:2982146-3021346	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2471350	GRK4	cis	lung	GTEx
rs2471350	GRK4	cis	Skin Sun Exposed Lower leg	GTEx
rs2471350	GRK4	Cis_1M	lymphoblastoid	RTeQTL
rs2471350	GRK4	cis	Thyroid	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2979600-3025000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr4:2983600-3032000	Weak transcription	Fetal Brain Female	brain
3	chr4:2991400-3024600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr4:3003800-3024600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:3005000-3018600	Weak transcription	Left Ventricle	heart
6	chr4:3005800-3038600	Weak transcription	Right Ventricle	heart
7	chr4:3007000-3020600	Weak transcription	Brain Germinal Matrix	brain
8	chr4:3007200-3015200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr4:3007600-3024600	Weak transcription	Brain Angular Gyrus	brain
10	chr4:3011200-3014400	Enhancers	Stomach Mucosa	stomach
11	chr4:3011800-3039600	Weak transcription	Right Atrium	heart
12	chr4:3012600-3015000	Weak transcription	GM12878-XiMat	blood
13	chr4:3012800-3024800	Weak transcription	Aorta	Aorta
14	chr4:3013200-3022600	Weak transcription	Ovary	ovary
15	chr4:3013400-3022200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:3013600-3015200	Weak transcription	Fetal Intestine Large	intestine
17	chr4:3013600-3015200	Weak transcription	Fetal Intestine Small	intestine
18	chr4:3013600-3018600	Weak transcription	HSMMtube	muscle
19	chr4:3013800-3015200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:3013800-3015200	Weak transcription	Fetal Lung	lung
21	chr4:3013800-3015200	Weak transcription	Gastric	stomach
22	chr4:3013800-3015200	Weak transcription	Pancreas	Pancrea
23	chr4:3013800-3018600	Weak transcription	HSMM	muscle
24	chr4:3013800-3022600	Weak transcription	Adipose Nuclei	Adipose

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