Variant report

Variant	rs6502498
Chromosome Location	chr17:16198975-16198976
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:16188284..16190570-chr17:16196788..16199758,2	MCF-7	breast:
2	chr17:16194799..16198455-chr17:16198846..16202251,3	K562	blood:
3	chr17:16115990..16118934-chr17:16198815..16201577,2	MCF-7	breast:
4	chr17:16198554..16200969-chr17:16344416..16346385,2	K562	blood:
5	chr17:16188324..16192785-chr17:16195612..16200767,7	K562	blood:

Variant related genes	Relation type
ENSG00000175061	Chromatin interaction
ENSG00000141027	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1029809	0.82[EUR][1000 genomes]
rs10852834	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11078337	0.90[EUR][1000 genomes]
rs11650283	0.86[ASN][1000 genomes]
rs11650427	0.83[EUR][1000 genomes]
rs11650956	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11651578	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11651955	0.91[ASN][1000 genomes]
rs11653650	0.82[EUR][1000 genomes]
rs11654658	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655325	0.81[EUR][1000 genomes]
rs11656811	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11868284	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12150564	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12936233	0.81[EUR][1000 genomes]
rs12936529	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12938394	0.82[EUR][1000 genomes]
rs12938397	0.89[EUR][1000 genomes]
rs12938878	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12939078	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12945855	0.81[EUR][1000 genomes]
rs12945877	0.89[ASN][1000 genomes]
rs12946717	0.89[ASN][1000 genomes]
rs12948244	0.81[EUR][1000 genomes]
rs12948905	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1476810	0.91[ASN][1000 genomes]
rs15739	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1963811	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2014604	0.81[EUR][1000 genomes]
rs2109262	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2324306	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2324307	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35762856	0.89[ASN][1000 genomes]
rs3785620	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3785622	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3785623	0.82[EUR][1000 genomes]
rs3785625	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3785626	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4791665	0.82[EUR][1000 genomes]
rs4792728	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4792729	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4792730	0.81[EUR][1000 genomes]
rs4792731	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4792732	0.88[ASN][1000 genomes]
rs56326304	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62072528	0.82[EUR][1000 genomes]
rs7210990	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7215071	0.81[EUR][1000 genomes]
rs7219687	0.81[EUR][1000 genomes]
rs7225920	0.82[EUR][1000 genomes]
rs8074727	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9303135	0.82[EUR][1000 genomes]
rs9747114	0.81[EUR][1000 genomes]
rs9909022	0.82[EUR][1000 genomes]
rs9910148	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9914734	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9916220	0.82[EUR][1000 genomes]
rs9944524	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv907715	chr17:16019978-16206540	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
6	nsv907717	chr17:16076898-16239832	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
7	esv3326983	chr17:16138963-16210147	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	21 gene(s)	inside rSNPs	diseases
8	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6502498	ADORA2B	cis	Esophagus Muscularis	GTEx
rs6502498	ADORA2B	cis	Artery Tibial	GTEx
rs6502498	ADORA2B	cis	Muscle Skeletal	GTEx
rs6502498	ZSWIM7	cis	Muscle Skeletal	GTEx
rs6502498	NCOR1	Cis_1M	lymphoblastoid	RTeQTL
rs6502498	CENPV	cis	Artery Tibial	GTEx
rs6502498	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs6502498	PRR6	cis	multi-tissue	Pritchard
rs6502498	ADORA2B	cis	Thyroid	GTEx
rs6502498	TTC19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16166200-16205400	Weak transcription	Brain Hippocampus Middle	brain
2	chr17:16181200-16205400	Weak transcription	Dnd41	blood
3	chr17:16187200-16205200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr17:16189400-16216600	Weak transcription	Fetal Brain Female	brain
5	chr17:16189800-16200400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr17:16190200-16200800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr17:16190200-16200800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:16190200-16200800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr17:16190200-16201000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr17:16190400-16203000	Weak transcription	Left Ventricle	heart
11	chr17:16190600-16203000	Weak transcription	Ovary	ovary
12	chr17:16190600-16205000	Weak transcription	Lung	lung
13	chr17:16190600-16205200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr17:16190600-16229600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr17:16190800-16200400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr17:16190800-16200600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr17:16190800-16201000	Weak transcription	Spleen	Spleen
18	chr17:16190800-16203000	Weak transcription	Fetal Muscle Leg	muscle
19	chr17:16190800-16204200	Weak transcription	Brain Anterior Caudate	brain
20	chr17:16190800-16205000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr17:16190800-16205200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr17:16190800-16205200	Weak transcription	NHEK	skin
23	chr17:16190800-16216400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr17:16190800-16220800	Weak transcription	Aorta	Aorta
25	chr17:16191000-16203000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr17:16191200-16200600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr17:16191200-16200800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr17:16191400-16203200	Weak transcription	Fetal Stomach	stomach
29	chr17:16191400-16205200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr17:16191400-16218400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr17:16191400-16219400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr17:16191400-16226000	Weak transcription	HSMMtube	muscle
33	chr17:16191600-16199400	Weak transcription	HMEC	breast
34	chr17:16191600-16200600	Weak transcription	Fetal Lung	lung
35	chr17:16191600-16203200	Weak transcription	Adipose Nuclei	Adipose
36	chr17:16191600-16204000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr17:16191600-16205200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr17:16191600-16216800	Weak transcription	Fetal Kidney	kidney
39	chr17:16191800-16203000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr17:16191800-16204000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr17:16191800-16205000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr17:16191800-16205000	Weak transcription	Placenta	Placenta
43	chr17:16191800-16205400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr17:16191800-16217200	Weak transcription	HSMM	muscle
45	chr17:16192600-16203200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr17:16192600-16205200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr17:16192800-16200600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr17:16192800-16201200	Weak transcription	Thymus	Thymus
49	chr17:16192800-16203200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr17:16192800-16229000	Weak transcription	Monocytes-CD14+_RO01746	blood

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