Variant report

Variant	rs56109540
Chromosome Location	chr7:69128429-69128430
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2865803	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55666499	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55752344	0.92[EUR][1000 genomes]
rs55772034	0.92[EUR][1000 genomes]
rs55773107	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56166692	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6946791	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949804	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6950764	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6954630	1.00[ASN][1000 genomes]
rs6973940	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs733883	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7781283	1.00[ASN][1000 genomes]
rs7786101	1.00[ASN][1000 genomes]
rs7810785	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv1023885	chr7:68894896-69158290	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv538915	chr7:68894896-69158290	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv916011	chr7:68942155-69330800	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv428169	chr7:69021482-69196743	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv831021	chr7:69122169-69364491	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69121400-69129400	Weak transcription	Psoas Muscle	Psoas
2	chr7:69122400-69128600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr7:69122600-69128800	Weak transcription	Brain Hippocampus Middle	brain
4	chr7:69122600-69128800	Weak transcription	Fetal Kidney	kidney
5	chr7:69122600-69135000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr7:69125000-69142000	Weak transcription	Fetal Stomach	stomach
7	chr7:69125000-69142400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr7:69125200-69130200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:69125200-69135200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr7:69125400-69128600	Weak transcription	Brain Anterior Caudate	brain
11	chr7:69125600-69132000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr7:69126000-69128600	Weak transcription	Ovary	ovary
13	chr7:69126000-69130600	Enhancers	Fetal Brain Female	brain
14	chr7:69126000-69134800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr7:69126200-69130200	Enhancers	Fetal Brain Male	brain
16	chr7:69127000-69130200	Enhancers	Brain Germinal Matrix	brain
17	chr7:69127400-69128600	Enhancers	GM12878-XiMat	blood
18	chr7:69127400-69129000	Enhancers	Fetal Lung	lung
19	chr7:69127600-69128600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:69127600-69128600	Weak transcription	Brain Substantia Nigra	brain
21	chr7:69127800-69129600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr7:69128000-69135000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr7:69128200-69129200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr7:69128200-69129400	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr7:69128400-69128600	Weak transcription	Brain Angular Gyrus	brain
26	chr7:69128400-69129200	Enhancers	Primary B cells from cord blood	blood
27	chr7:69128400-69129200	Enhancers	Colon Smooth Muscle	Colon
28	chr7:69128400-69130600	Enhancers	Primary B cells from peripheral blood	blood

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