Variant report

Variant	rs939492
Chromosome Location	chr15:77865811-77865812
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77864365..77867025-chr15:77869640..77872108,2	MCF-7	breast:
2	chr15:77860363..77863668-chr15:77864267..77867089,3	K562	blood:

Variant related genes	Relation type
ENSG00000259420	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs12593111	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2460770	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2667760	0.80[EUR][1000 genomes]
rs2667761	0.81[EUR][1000 genomes]
rs2667762	0.81[EUR][1000 genomes]
rs2667763	0.82[EUR][1000 genomes]
rs2667766	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2667768	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2667769	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2667770	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2667771	0.85[ASN][1000 genomes]
rs2667772	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2667773	0.92[ASN][1000 genomes]
rs2667774	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2667776	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2667777	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2667778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2667779	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2667780	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2682906	0.80[EUR][1000 genomes]
rs2682908	0.81[EUR][1000 genomes]
rs2682909	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2682911	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2682912	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2682913	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2682914	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2682915	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2682916	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2682918	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2682919	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2682920	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2682922	0.81[AFR][1000 genomes]
rs2682923	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2682925	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2682926	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28393270	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28612444	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35971869	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs867908	0.81[EUR][1000 genomes]
rs867917	0.81[EUR][1000 genomes]
rs867918	0.81[EUR][1000 genomes]
rs868297	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs868299	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs884141	0.81[EUR][1000 genomes]
rs907378	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs907379	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs907380	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs907381	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs907382	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs907384	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs939486	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs939487	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs939491	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs939493	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv904415	chr15:77845959-77943935	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv904416	chr15:77845959-77967416	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv904417	chr15:77851535-77935992	Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv904418	chr15:77851535-77963887	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77862000-77869400	Weak transcription	Brain Anterior Caudate	brain
2	chr15:77862200-77868200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr15:77862200-77869000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr15:77862200-77875000	Weak transcription	Left Ventricle	heart
5	chr15:77862400-77866600	Weak transcription	Lung	lung
6	chr15:77862400-77867200	Weak transcription	Stomach Mucosa	stomach
7	chr15:77862400-77868000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr15:77862400-77868800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:77862400-77869400	Weak transcription	Brain Angular Gyrus	brain
10	chr15:77862400-77869400	Weak transcription	Brain Substantia Nigra	brain
11	chr15:77862600-77868000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:77862600-77869400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:77862800-77867800	Weak transcription	Fetal Intestine Small	intestine
14	chr15:77862800-77868400	Weak transcription	Fetal Muscle Leg	muscle
15	chr15:77862800-77869600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:77864000-77869600	Weak transcription	Fetal Stomach	stomach
17	chr15:77864000-77871400	Weak transcription	Spleen	Spleen
18	chr15:77864400-77866000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:77864800-77866600	Enhancers	Brain Hippocampus Middle	brain
20	chr15:77865000-77866200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:77865600-77866800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:77865800-77866000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:77865800-77866400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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