Variant report

Variant	rs17383984
Chromosome Location	chr15:77579094-77579095
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	chr15:77543946..77545839-chr15:77577547..77579797,2	MCF-7	breast:
2	chr15:77576555..77578246-chr15:77578519..77580387,2	K562	blood:

Variant related genes	Relation type
ENSG00000173517	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10519164	0.85[ASN][1000 genomes]
rs10519167	0.82[ASN][1000 genomes]
rs11630837	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11630843	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632999	0.91[ASN][1000 genomes]
rs11633318	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11634056	1.00[ASN][1000 genomes]
rs11636803	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11637488	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11638220	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11639079	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11639197	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11639308	0.85[ASN][1000 genomes]
rs12899552	0.83[ASN][1000 genomes]
rs12909704	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12910419	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1554051	0.85[ASN][1000 genomes]
rs17382798	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17383727	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17384406	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17385648	0.85[ASN][1000 genomes]
rs17466989	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17468792	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17469276	0.83[ASN][1000 genomes]
rs17470228	0.85[ASN][1000 genomes]
rs2100054	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2864082	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34672572	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34870981	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34981488	0.82[ASN][1000 genomes]
rs35490414	0.85[ASN][1000 genomes]
rs35598964	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35902242	0.82[ASN][1000 genomes]
rs4450362	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55716459	0.82[ASN][1000 genomes]
rs56060493	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62007263	0.85[ASN][1000 genomes]
rs62008430	0.94[ASN][1000 genomes]
rs62008432	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62008434	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62008455	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66715204	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71405237	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71407208	0.85[ASN][1000 genomes]
rs7166293	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7176254	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181345	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7182880	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8030500	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8032925	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[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	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	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	esv1832234	chr15:77451350-77694607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	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
6	nsv1041064	chr15:77497903-77631698	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1051744	chr15:77511489-77679160	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1044270	chr15:77534919-77611256	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv542445	chr15:77534919-77611256	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv1830237	chr15:77535785-77694607	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv33934	chr15:77548764-77579524	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv482689	chr15:77576396-77731559	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17383984	RP11-797A18.4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77528800-77579200	Weak transcription	Brain Angular Gyrus	brain
2	chr15:77541800-77589800	Weak transcription	Fetal Intestine Small	intestine
3	chr15:77542200-77580000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:77544400-77581000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr15:77544600-77589200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr15:77559800-77579400	Weak transcription	Brain Anterior Caudate	brain
7	chr15:77559800-77585200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr15:77562000-77580200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr15:77562200-77589600	Weak transcription	Primary T cells from cord blood	blood
10	chr15:77567600-77580200	Weak transcription	Fetal Lung	lung
11	chr15:77570000-77579400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr15:77571800-77579400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr15:77571800-77579600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr15:77571800-77585600	Weak transcription	Right Ventricle	heart
15	chr15:77572000-77582000	Weak transcription	Left Ventricle	heart
16	chr15:77572200-77580000	Weak transcription	HSMMtube	muscle
17	chr15:77572600-77580800	Weak transcription	Fetal Muscle Leg	muscle
18	chr15:77573600-77580600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr15:77573600-77589400	Weak transcription	Fetal Stomach	stomach
20	chr15:77574600-77580800	Weak transcription	Fetal Brain Male	brain
21	chr15:77574600-77585200	Weak transcription	Psoas Muscle	Psoas
22	chr15:77575000-77585400	Weak transcription	NH-A	brain
23	chr15:77575400-77580400	Weak transcription	Brain Hippocampus Middle	brain
24	chr15:77575400-77586000	Weak transcription	HepG2	liver
25	chr15:77575600-77579200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr15:77575600-77579400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr15:77575600-77580000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr15:77576400-77579200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr15:77576400-77583200	Weak transcription	Fetal Heart	heart
30	chr15:77576600-77579600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:77576600-77579800	Weak transcription	NHLF	lung
32	chr15:77576800-77580200	Weak transcription	Liver	Liver
33	chr15:77577000-77579200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr15:77577000-77579400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr15:77577000-77579800	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr15:77577000-77580000	Weak transcription	Adipose Nuclei	Adipose
37	chr15:77577000-77580000	Weak transcription	Fetal Intestine Large	intestine
38	chr15:77577200-77579400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:77577200-77619400	Weak transcription	HSMM	muscle
40	chr15:77577600-77579200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr15:77577600-77579200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr15:77577600-77579200	Weak transcription	Dnd41	blood
43	chr15:77577600-77579800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr15:77577600-77579800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr15:77577800-77579400	Weak transcription	Osteobl	bone
46	chr15:77577800-77587200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:77577800-77590000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr15:77578000-77579200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:77578000-77579600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:77578000-77579800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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