Variant report

Variant	rs1972347
Chromosome Location	chr13:48548005-48548006
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11148099	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11618397	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1326135	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1326136	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1536301	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1886976	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1926089	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2148243	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2148245	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2296574	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2406698	0.80[ASN][1000 genomes]
rs2406699	0.83[ASN][1000 genomes]
rs4942725	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4942727	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4942729	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4942735	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61973260	0.80[ASN][1000 genomes]
rs6561417	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6561419	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6561420	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6561424	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6561427	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs718010	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7320366	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7320461	0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7320759	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7322515	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7326984	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7327260	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7328549	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7329419	0.81[ASN][1000 genomes]
rs7333659	0.81[ASN][1000 genomes]
rs7333821	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7334207	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7335788	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7337744	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7338125	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7338894	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs765809	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7990505	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9316339	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9526423	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9526424	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9526426	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9526429	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9534877	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9534878	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9534879	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9534880	0.80[ASN][1000 genomes]
rs9534882	0.85[AFR][1000 genomes]
rs9534885	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9534889	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9534892	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9534896	0.85[AFR][1000 genomes]
rs9534897	0.82[AFR][1000 genomes]
rs9534901	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9534919	0.81[ASN][1000 genomes]
rs9562787	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9567959	0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9567960	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9567963	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9595825	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933980	chr13:48431000-48557419	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1972347	SUCLA2	Cis_1M	lymphoblastoid	RTeQTL
rs1972347	MED4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48507200-48548800	Weak transcription	Stomach Mucosa	stomach
2	chr13:48514400-48574000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr13:48532000-48551400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr13:48532200-48565200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr13:48532400-48559400	Weak transcription	Gastric	stomach
6	chr13:48532400-48565200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr13:48534000-48560800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr13:48534200-48573200	Weak transcription	Brain Angular Gyrus	brain
9	chr13:48534400-48574400	Weak transcription	Small Intestine	intestine
10	chr13:48534600-48550400	Weak transcription	Right Ventricle	heart
11	chr13:48535000-48564800	Weak transcription	NHLF	lung
12	chr13:48535200-48552000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr13:48536000-48550400	Weak transcription	Fetal Heart	heart
14	chr13:48536200-48550000	Weak transcription	NHEK	skin
15	chr13:48537200-48574200	Weak transcription	Colonic Mucosa	Colon
16	chr13:48537400-48560200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr13:48537400-48574000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr13:48537400-48574400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:48538000-48567200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr13:48538400-48551000	Weak transcription	Fetal Brain Male	brain
21	chr13:48538400-48551600	Weak transcription	Brain Hippocampus Middle	brain
22	chr13:48538400-48574000	Weak transcription	Hela-S3	cervix
23	chr13:48538600-48559800	Weak transcription	HUVEC	blood vessel
24	chr13:48538800-48564800	Weak transcription	Brain Germinal Matrix	brain
25	chr13:48539400-48551800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr13:48539600-48571200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr13:48540000-48574200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr13:48540200-48552600	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr13:48540200-48559000	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr13:48540600-48550000	Weak transcription	HSMMtube	muscle
31	chr13:48540800-48548400	Weak transcription	NHDF-Ad	bronchial
32	chr13:48540800-48565000	Weak transcription	NH-A	brain
33	chr13:48541200-48549200	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr13:48541800-48550000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr13:48542000-48558800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr13:48542400-48551600	Weak transcription	HMEC	breast
37	chr13:48542400-48564800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr13:48542400-48565200	Weak transcription	Psoas Muscle	Psoas
39	chr13:48542400-48567000	Weak transcription	Esophagus	oesophagus
40	chr13:48542600-48549800	Weak transcription	Ovary	ovary
41	chr13:48542800-48553800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr13:48542800-48559000	Weak transcription	HSMM	muscle
43	chr13:48543000-48553600	Weak transcription	Fetal Kidney	kidney
44	chr13:48543000-48574400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr13:48543400-48560600	Weak transcription	HepG2	liver
46	chr13:48544000-48550400	Weak transcription	GM12878-XiMat	blood
47	chr13:48544000-48551400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr13:48545000-48548800	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr13:48545000-48550800	Strong transcription	Fetal Muscle Trunk	muscle
50	chr13:48545200-48548800	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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