Variant report

Variant	rs13195462
Chromosome Location	chr6:109966893-109966894
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10499052	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11964533	0.80[EUR][1000 genomes]
rs11968891	0.80[AMR][1000 genomes]
rs12529505	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12661287	0.80[EUR][1000 genomes]
rs13191995	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13199088	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13203636	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13204787	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13207864	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13211604	0.82[EUR][1000 genomes]
rs13212535	0.82[EUR][1000 genomes]
rs13214717	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28823411	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs731878	0.91[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13195462	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs13195462	SMPD2	cis	Whole Blood	GTEx
rs13195462	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs13195462	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 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	chr6:109961600-109967600	Weak transcription	Brain Angular Gyrus	brain
9	chr6:109961600-109971400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr6:109961600-110000600	Weak transcription	Thymus	Thymus
11	chr6:109961800-109968600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr6:109961800-109981000	Weak transcription	Right Ventricle	heart
13	chr6:109962000-109983400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr6:109962600-109967000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr6:109964400-109967000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr6:109965000-109967000	Weak transcription	Left Ventricle	heart
17	chr6:109965200-109967800	Strong transcription	Stomach Smooth Muscle	stomach
18	chr6:109965200-109992200	Weak transcription	Fetal Brain Female	brain
19	chr6:109965200-110000600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr6:109965400-109968400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:109965600-109983200	Weak transcription	Brain Substantia Nigra	brain
22	chr6:109965600-109983200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr6:109965600-109990800	Weak transcription	Primary B cells from cord blood	blood
24	chr6:109966000-109967200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
25	chr6:109966000-109977000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:109966200-109967200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:109966200-109967200	ZNF genes & repeats	Fetal Intestine Small	intestine
28	chr6:109966400-109967200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
29	chr6:109966400-109967200	ZNF genes & repeats	Aorta	Aorta
30	chr6:109966600-109969000	Weak transcription	Pancreas	Pancrea
31	chr6:109966800-109967200	ZNF genes & repeats	Gastric	stomach
32	chr6:109966800-109967400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:109966800-109991000	Weak transcription	Ovary	ovary
34	chr6:109966800-109993200	Weak transcription	Adipose Nuclei	Adipose

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