Variant report

Variant	rs72800377
Chromosome Location	chr10:54790340-54790341
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10508984	0.91[EUR][1000 genomes]
rs10740531	0.90[EUR][1000 genomes]
rs10824856	0.90[EUR][1000 genomes]
rs10824857	0.93[EUR][1000 genomes]
rs10824859	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10824860	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11003335	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11003336	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11003339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11003340	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11003341	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11003343	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11812875	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11819148	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12360114	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1917190	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1917194	0.90[EUR][1000 genomes]
rs1917195	0.90[EUR][1000 genomes]
rs1917196	0.90[EUR][1000 genomes]
rs1917197	0.91[EUR][1000 genomes]
rs1917205	0.89[EUR][1000 genomes]
rs1949813	0.90[EUR][1000 genomes]
rs1949814	0.91[EUR][1000 genomes]
rs2248319	0.89[EUR][1000 genomes]
rs2248678	0.89[EUR][1000 genomes]
rs2253152	0.91[EUR][1000 genomes]
rs2253266	0.91[EUR][1000 genomes]
rs2253468	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2264663	0.91[EUR][1000 genomes]
rs2265880	0.89[EUR][1000 genomes]
rs2462479	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492354	0.83[EUR][1000 genomes]
rs2891426	0.84[EUR][1000 genomes]
rs7069155	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72800376	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895404	chr10:54545590-54850707	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1043809	chr10:54645158-54860817	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv540627	chr10:54645158-54860817	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv467201	chr10:54697623-54929003	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv550906	chr10:54697623-54929003	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv470939	chr10:54700783-54917339	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv467202	chr10:54735164-54830687	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv550907	chr10:54735164-54830687	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv895405	chr10:54765608-54824741	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv508585	chr10:54769376-54796804	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv895406	chr10:54780677-54830687	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv3509840	chr10:54782746-54790644	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv1821304	chr10:54784919-54794208	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	esv1828095	chr10:54784919-54794208	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	esv1851757	chr10:54784919-54794208	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv437674	chr10:54787062-54793330	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv437675	chr10:54787838-54793330	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv437676	chr10:54787838-54793330	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs72800377	RP11-319F12.2	cis	Thyroid	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54786000-54790400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr10:54789200-54791000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr10:54789200-54791000	Enhancers	Placenta	Placenta
4	chr10:54789200-54791200	Enhancers	Fetal Intestine Large	intestine
5	chr10:54789200-54792000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr10:54789400-54791000	Enhancers	GM12878-XiMat	blood
7	chr10:54789400-54791000	Enhancers	HepG2	liver
8	chr10:54789400-54791000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr10:54789400-54791200	Enhancers	Primary hematopoietic stem cells	blood
10	chr10:54789400-54791200	Enhancers	Placenta Amnion	Placenta Amnion
11	chr10:54789400-54791200	Enhancers	NHEK	skin
12	chr10:54789600-54790600	Enhancers	Hela-S3	cervix
13	chr10:54789600-54790800	Enhancers	H1 Cell Line	embryonic stem cell
14	chr10:54789600-54790800	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr10:54789600-54790800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr10:54789600-54790800	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr10:54789600-54790800	Flanking Active TSS	Fetal Kidney	kidney
18	chr10:54789600-54791000	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr10:54789600-54791000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr10:54789600-54791000	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr10:54789600-54791000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr10:54789600-54791000	Enhancers	Duodenum Mucosa	Duodenum
23	chr10:54789600-54791200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr10:54789600-54791400	Enhancers	Fetal Intestine Small	intestine
25	chr10:54789800-54790400	Enhancers	Fetal Lung	lung
26	chr10:54789800-54790600	Enhancers	Stomach Mucosa	stomach
27	chr10:54789800-54790800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr10:54789800-54791000	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr10:54790000-54791000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr10:54790000-54791200	Enhancers	HUVEC	blood vessel
31	chr10:54790000-54793800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr10:54790200-54790600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr10:54790200-54790600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr10:54790200-54790800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr10:54790200-54791000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr10:54790200-54791200	Enhancers	Rectal Mucosa Donor 31	rectum

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