Variant report

Variant	rs6772424
Chromosome Location	chr3:49697290-49697291
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49689149..49690759-chr3:49696566..49699118,2	MCF-7	breast:
2	chr3:49683730..49686310-chr3:49694623..49697344,2	K562	blood:
3	chr3:49696156..49697699-chr3:49699685..49702329,2	K562	blood:
4	chr3:49686939..49689819-chr3:49694987..49697482,3	K562	blood:
5	chr3:49692557..49695164-chr3:49696154..49698267,2	K562	blood:
6	chr3:49507003..49509478-chr3:49697211..49699386,2	K562	blood:

Variant related genes	Relation type
ENSG00000173402	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs34379671	1.00[AMR][1000 genomes]
rs34630302	1.00[AMR][1000 genomes]
rs35481257	1.00[AMR][1000 genomes]
rs6777731	1.00[AMR][1000 genomes]
rs6797615	1.00[AMR][1000 genomes]
rs6800591	1.00[AMR][1000 genomes]
rs6806073	1.00[AMR][1000 genomes]
rs6808633	1.00[AMR][1000 genomes]
rs72938200	1.00[AMR][1000 genomes]
rs7615240	1.00[AMR][1000 genomes]
rs7616171	1.00[AMR][1000 genomes]
rs7623582	1.00[AMR][1000 genomes]
rs7626820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7633189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7634945	1.00[AMR][1000 genomes]
rs7636222	1.00[AMR][1000 genomes]
rs7637266	1.00[AMR][1000 genomes]
rs7641976	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7648632	1.00[AMR][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	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1011428	chr3:49649989-49706068	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49685200-49708200	Strong transcription	Brain Germinal Matrix	brain
2	chr3:49685400-49708400	Strong transcription	Fetal Brain Female	brain
3	chr3:49686600-49710600	Weak transcription	Right Atrium	heart
4	chr3:49687600-49702400	Weak transcription	Right Ventricle	heart
5	chr3:49687600-49705800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:49690400-49702000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:49690400-49710600	Weak transcription	Brain Substantia Nigra	brain
8	chr3:49692200-49710400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:49692400-49700800	Weak transcription	Brain Anterior Caudate	brain
10	chr3:49693200-49703200	Weak transcription	Gastric	stomach
11	chr3:49693400-49698600	Weak transcription	Spleen	Spleen
12	chr3:49694000-49698000	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:49694200-49698600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:49694600-49697400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:49694800-49698800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:49695000-49702000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:49695200-49710600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:49695800-49704000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:49696200-49700800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:49696400-49700400	Weak transcription	Brain Angular Gyrus	brain
21	chr3:49696600-49698800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:49696600-49701400	Weak transcription	HepG2	liver
23	chr3:49696600-49701800	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:49697200-49697400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:49697200-49699000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:49697200-49699600	Enhancers	Pancreas	Pancrea

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