Variant report

Variant	rs13104559
Chromosome Location	chr4:2968055-2968056
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:2963799..2967429-chr4:2967585..2973552,6	K562	blood:
2	chr4:2965936..2968451-chr4:2977512..2979704,2	K562	blood:
3	chr4:2965958..2968897-chr4:2971775..2974450,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125388	Chromatin interaction
ENSG00000087269	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12512648	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12696706	0.88[EUR][1000 genomes]
rs13103004	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13104987	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13109886	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13111777	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13123779	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13132131	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1419043	0.81[ASN][1000 genomes]
rs1978031	0.80[ASN][1000 genomes]
rs1978032	0.80[ASN][1000 genomes]
rs34020100	0.88[EUR][1000 genomes]
rs34163500	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34540265	0.87[ASN][1000 genomes]
rs35163447	0.88[EUR][1000 genomes]
rs35781129	0.87[ASN][1000 genomes]
rs35909590	0.87[ASN][1000 genomes]
rs60504719	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60635068	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6856669	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73189480	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv1014013	chr4:2959876-3009507	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv536999	chr4:2959876-3009507	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	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
12	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
13	nsv1003528	chr4:2964261-3011568	Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv537000	chr4:2964261-3011568	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2966200-2968200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:2966200-2970400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:2966200-2972200	Weak transcription	Aorta	Aorta
4	chr4:2966200-2977400	Weak transcription	Lung	lung
5	chr4:2966400-2968200	Weak transcription	Psoas Muscle	Psoas
6	chr4:2966400-2968800	Weak transcription	Fetal Intestine Small	intestine
7	chr4:2966400-2969400	Weak transcription	Placenta	Placenta
8	chr4:2966400-2970400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:2966400-2973200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:2966400-2974000	Weak transcription	Right Ventricle	heart
11	chr4:2966400-2974800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:2966400-2975600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:2966400-2978600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr4:2966400-2980200	Weak transcription	Left Ventricle	heart
15	chr4:2966400-2980200	Weak transcription	Ovary	ovary
16	chr4:2966400-2980400	Weak transcription	Spleen	Spleen
17	chr4:2966600-2968400	Weak transcription	HMEC	breast
18	chr4:2966600-2969800	Weak transcription	HUVEC	blood vessel
19	chr4:2966600-2970400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:2966600-2970800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr4:2966600-2977600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr4:2966600-2978600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:2966600-2978800	Weak transcription	NH-A	brain
24	chr4:2966600-2979000	Weak transcription	HSMM	muscle
25	chr4:2966600-2979600	Weak transcription	Primary T cells from cord blood	blood
26	chr4:2966600-2982000	Weak transcription	Brain Germinal Matrix	brain
27	chr4:2966600-2982200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr4:2966800-2969000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:2966800-2971800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:2966800-2974600	Weak transcription	Fetal Brain Female	brain
31	chr4:2966800-2975200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr4:2966800-2977200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:2966800-2978800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:2966800-2978800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:2966800-2979000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:2966800-2979200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:2966800-2979400	Weak transcription	Brain Substantia Nigra	brain
38	chr4:2966800-2982200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr4:2967000-2978800	Weak transcription	Osteobl	bone
40	chr4:2967000-2979200	Weak transcription	Brain Anterior Caudate	brain
41	chr4:2967200-2968400	Weak transcription	Fetal Brain Male	brain
42	chr4:2967200-2969200	Strong transcription	Fetal Muscle Leg	muscle
43	chr4:2967200-2970400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr4:2967200-2976200	Weak transcription	Dnd41	blood
45	chr4:2967200-2978600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:2967200-2978600	Weak transcription	HSMMtube	muscle
47	chr4:2967200-2978800	Weak transcription	NHDF-Ad	bronchial
48	chr4:2967200-2979000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr4:2967200-2979000	Weak transcription	NHLF	lung
50	chr4:2967200-2979200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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