Variant report

Variant	rs2891657
Chromosome Location	chr19:38197084-38197085
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1060522	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10853710	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11083433	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11666172	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11668796	0.87[EUR][1000 genomes]
rs11671953	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11673497	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16975299	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17246792	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28431170	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34991303	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55871826	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55913702	0.87[EUR][1000 genomes]
rs55950325	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62108305	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62108351	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6508739	0.87[EUR][1000 genomes]
rs7249622	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7253081	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258385	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73037060	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2891657	AC012309.5	cis	Thyroid	GTEx
rs2891657	ZNF573	cis	multi-tissue	Pritchard

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38183200-38208800	Weak transcription	Fetal Heart	heart
2	chr19:38184200-38201200	Weak transcription	Colonic Mucosa	Colon
3	chr19:38184400-38208800	Weak transcription	HepG2	liver
4	chr19:38187000-38207800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:38187000-38208000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:38187400-38199000	ZNF genes & repeats	A549	lung
7	chr19:38187400-38205800	Strong transcription	Dnd41	blood
8	chr19:38187400-38208000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:38188000-38198200	Weak transcription	Pancreas	Pancrea
10	chr19:38188200-38197800	Weak transcription	Right Ventricle	heart
11	chr19:38188200-38209200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:38188400-38202000	Weak transcription	Placenta	Placenta
13	chr19:38189400-38209200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr19:38190000-38206600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr19:38190400-38197200	Weak transcription	Small Intestine	intestine
16	chr19:38190600-38197200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:38190600-38197200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr19:38190600-38197200	Weak transcription	Brain Hippocampus Middle	brain
19	chr19:38190600-38197200	Weak transcription	Fetal Muscle Leg	muscle
20	chr19:38190600-38197400	Weak transcription	Thymus	Thymus
21	chr19:38190600-38198000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr19:38190600-38198400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:38190600-38198400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr19:38190600-38209000	Weak transcription	Brain Substantia Nigra	brain
25	chr19:38190600-38209200	Weak transcription	HSMMtube	muscle
26	chr19:38190800-38197200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr19:38190800-38197200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr19:38190800-38197200	Weak transcription	Fetal Intestine Large	intestine
29	chr19:38190800-38197200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr19:38190800-38198200	Weak transcription	Brain Angular Gyrus	brain
31	chr19:38190800-38198200	Weak transcription	Osteobl	bone
32	chr19:38190800-38198600	Weak transcription	HSMM	muscle
33	chr19:38190800-38202200	Weak transcription	NH-A	brain
34	chr19:38190800-38209000	Weak transcription	Stomach Mucosa	stomach
35	chr19:38190800-38209200	Weak transcription	Fetal Thymus	thymus
36	chr19:38190800-38209200	Weak transcription	Psoas Muscle	Psoas
37	chr19:38191000-38197600	Weak transcription	Brain Anterior Caudate	brain
38	chr19:38191000-38197800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr19:38191000-38197800	Weak transcription	Fetal Brain Male	brain
40	chr19:38191000-38198000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr19:38191200-38197200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr19:38191200-38198400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr19:38191200-38209200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr19:38191200-38209200	Weak transcription	Colon Smooth Muscle	Colon
45	chr19:38191600-38197200	Weak transcription	Fetal Kidney	kidney
46	chr19:38191600-38202000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr19:38192200-38203000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:38192600-38197200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr19:38192600-38198200	Weak transcription	Aorta	Aorta
50	chr19:38192600-38198400	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links