Variant report

Variant	rs13199109
Chromosome Location	chr6:109973505-109973506
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10457192	0.82[EUR][1000 genomes]
rs10457194	0.82[EUR][1000 genomes]
rs10457195	0.84[EUR][1000 genomes]
rs10457203	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10499053	0.84[ASN][1000 genomes]
rs10782163	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11153183	0.82[EUR][1000 genomes]
rs11153188	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11153213	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11153215	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11752791	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11754340	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11754455	0.82[EUR][1000 genomes]
rs11755641	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11758651	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12191353	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12192268	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12192776	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12193719	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12194061	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12194157	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12197180	0.82[EUR][1000 genomes]
rs12197838	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12197950	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12198938	0.82[EUR][1000 genomes]
rs12199154	0.82[EUR][1000 genomes]
rs12201356	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12201444	0.88[EUR][1000 genomes]
rs12204548	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12205140	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12205485	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12208018	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12208933	0.82[ASN][1000 genomes]
rs12210706	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12212476	0.82[EUR][1000 genomes]
rs12214639	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12215077	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12528781	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13191066	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13199135	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13201430	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13201947	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13201951	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13203587	0.82[EUR][1000 genomes]
rs13204102	0.81[ASN][1000 genomes]
rs13204500	0.86[ASN][1000 genomes]
rs1321328	0.90[ASN][1000 genomes]
rs13220915	0.82[EUR][1000 genomes]
rs1322124	0.88[EUR][1000 genomes]
rs1406899	0.82[EUR][1000 genomes]
rs1476388	0.82[EUR][1000 genomes]
rs1960325	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1980591	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2024849	0.82[EUR][1000 genomes]
rs2024850	0.82[EUR][1000 genomes]
rs2024852	0.82[EUR][1000 genomes]
rs2024853	0.82[EUR][1000 genomes]
rs2025148	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2208209	0.82[ASN][1000 genomes]
rs2273752	0.88[EUR][1000 genomes]
rs2277114	0.82[EUR][1000 genomes]
rs2357124	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36131450	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3799845	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3799849	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3899233	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4141930	0.88[EUR][1000 genomes]
rs4490694	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4945833	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4947016	0.88[EUR][1000 genomes]
rs6568592	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6911700	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6914498	0.82[ASN][1000 genomes]
rs71541003	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs729888	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7341297	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs749517	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7755941	0.82[EUR][1000 genomes]
rs7767525	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7773950	0.82[EUR][1000 genomes]
rs971434	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026012	chr6:109851638-109999379	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv604484	chr6:109851937-109997529	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1019389	chr6:109868058-109987502	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv538416	chr6:109868058-109987502	Genic enhancers ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv917318	chr6:109885195-109982375	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv949475	chr6:109907936-110160501	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv933105	chr6:109933270-110064342	ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv817322	chr6:109933272-110070574	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv830769	chr6:109944334-110078120	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv604485	chr6:109959269-110054486	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13199109	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs13199109	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs13199109	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs13199109	SMPD2	cis	Whole Blood	GTEx
rs13199109	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109933000-109985200	Weak transcription	Psoas Muscle	Psoas
2	chr6:109948000-109995000	Weak transcription	Brain Anterior Caudate	brain
3	chr6:109953800-109980800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:109954400-109994800	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:109959400-109975200	Weak transcription	Primary T cells from cord blood	blood
6	chr6:109960000-109984000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr6:109961400-110000800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:109961600-110000600	Weak transcription	Thymus	Thymus
9	chr6:109961800-109981000	Weak transcription	Right Ventricle	heart
10	chr6:109962000-109983400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:109965200-109992200	Weak transcription	Fetal Brain Female	brain
12	chr6:109965200-110000600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:109965600-109983200	Weak transcription	Brain Substantia Nigra	brain
14	chr6:109965600-109983200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:109965600-109990800	Weak transcription	Primary B cells from cord blood	blood
16	chr6:109966000-109977000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:109966800-109991000	Weak transcription	Ovary	ovary
18	chr6:109966800-109993200	Weak transcription	Adipose Nuclei	Adipose
19	chr6:109967200-109981800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr6:109967200-109986800	Weak transcription	Aorta	Aorta
21	chr6:109967200-109989800	Weak transcription	Gastric	stomach
22	chr6:109967200-109992600	Weak transcription	Left Ventricle	heart
23	chr6:109967800-109997000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr6:109968400-109974400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:109972400-109992200	Weak transcription	Liver	Liver

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