Variant report

Variant	rs2800475
Chromosome Location	chr10:38649452-38649453
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs17595369	0.82[ASN][1000 genomes]
rs17595376	0.82[ASN][1000 genomes]
rs2754358	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2754362	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2754369	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2754373	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2800483	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2800542	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2804633	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2804634	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2804645	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2804676	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9340228	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[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	nsv895030	chr10:37715737-38674609	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv540566	chr10:38301001-38680127	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv33710	chr10:38545898-38671289	Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv427860	chr10:38588021-38818835	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv895034	chr10:38632352-38743545	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv947859	chr10:38633447-38674546	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv2764202	chr10:38641508-39076221	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1048953	chr10:38645824-39074038	Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2800475	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL
rs2800475	ZNF37A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38645600-38655200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr10:38645600-38660000	Weak transcription	Spleen	Spleen
3	chr10:38645600-38660200	Weak transcription	Aorta	Aorta
4	chr10:38645600-38661600	Weak transcription	Small Intestine	intestine
5	chr10:38645800-38660000	Weak transcription	Esophagus	oesophagus
6	chr10:38645800-38660000	Weak transcription	Gastric	stomach
7	chr10:38645800-38660000	Weak transcription	Pancreas	Pancrea
8	chr10:38645800-38661000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr10:38645800-38662200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr10:38645800-38662400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr10:38645800-38669000	Weak transcription	Colon Smooth Muscle	Colon
12	chr10:38646000-38649600	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr10:38646000-38653200	Weak transcription	Fetal Muscle Leg	muscle
14	chr10:38646000-38653200	Weak transcription	A549	lung
15	chr10:38646000-38653800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr10:38646000-38654400	Weak transcription	Lung	lung
17	chr10:38646000-38655000	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr10:38646000-38655000	Weak transcription	Brain Germinal Matrix	brain
19	chr10:38646000-38655000	Weak transcription	Thymus	Thymus
20	chr10:38646000-38655400	Weak transcription	Fetal Intestine Large	intestine
21	chr10:38646000-38656000	Weak transcription	Left Ventricle	heart
22	chr10:38646000-38660000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr10:38646000-38660000	Weak transcription	Ovary	ovary
24	chr10:38646000-38661600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr10:38646000-38661800	Weak transcription	HSMM	muscle
26	chr10:38646000-38662200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr10:38646000-38665200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr10:38646000-38670600	Weak transcription	Fetal Stomach	stomach
29	chr10:38646200-38651000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr10:38646200-38653800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr10:38646200-38653800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr10:38646200-38653800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr10:38646200-38657200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr10:38646200-38658400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr10:38646200-38660000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr10:38646200-38660200	Weak transcription	Brain Anterior Caudate	brain
37	chr10:38646200-38662400	Weak transcription	Osteobl	bone
38	chr10:38646200-38667000	Weak transcription	Fetal Intestine Small	intestine
39	chr10:38646200-38669200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr10:38646200-38669200	Weak transcription	Right Ventricle	heart
41	chr10:38646400-38649800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr10:38646400-38649800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr10:38646400-38650600	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr10:38646400-38651400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr10:38646400-38654400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr10:38646400-38654400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr10:38646400-38654400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr10:38646400-38654400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr10:38646400-38654800	Weak transcription	Primary B cells from cord blood	blood
50	chr10:38646400-38655200	Weak transcription	Brain Cingulate Gyrus	brain

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