Variant report

Variant	rs7564719
Chromosome Location	chr2:54829731-54829732
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10166844	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10169954	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10169975	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10170066	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10170355	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10176445	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10182538	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10182836	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10183043	0.94[ASN][1000 genomes]
rs10183867	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10184128	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10187338	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10188545	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10193692	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10205410	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10206143	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10208225	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10210502	0.92[ASN][1000 genomes]
rs1137645	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11892443	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11896957	0.81[ASN][1000 genomes]
rs11898032	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11898033	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11902987	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12713262	0.81[ASN][1000 genomes]
rs12713263	0.81[ASN][1000 genomes]
rs12713264	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12713265	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12713266	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12713267	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12713268	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12713269	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12713270	0.81[ASN][1000 genomes]
rs12713271	0.81[ASN][1000 genomes]
rs12713273	0.90[ASN][1000 genomes]
rs12713274	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12987967	0.83[ASN][1000 genomes]
rs13386146	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13391522	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13391803	0.90[ASN][1000 genomes]
rs13399656	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13403284	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13407214	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13423873	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13432302	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17046097	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28581481	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3287	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34077590	0.87[ASN][1000 genomes]
rs34094680	0.87[ASN][1000 genomes]
rs34978408	0.81[ASN][1000 genomes]
rs3796017	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3796018	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4346422	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4347868	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4358162	0.81[ASN][1000 genomes]
rs4374410	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4455200	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4519566	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4577321	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4616509	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4641979	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57281248	0.87[ASN][1000 genomes]
rs6545430	0.84[ASN][1000 genomes]
rs6706263	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6721612	0.81[ASN][1000 genomes]
rs6724136	0.85[ASN][1000 genomes]
rs6730876	0.81[ASN][1000 genomes]
rs6734445	0.90[ASN][1000 genomes]
rs6734536	0.87[ASN][1000 genomes]
rs6739140	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6740893	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6749802	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7340302	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7424459	0.94[ASN][1000 genomes]
rs7556752	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7584223	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7586066	0.90[ASN][1000 genomes]
rs7586311	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7591204	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7591231	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7599241	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7602992	0.89[ASN][1000 genomes]
rs7608414	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9677089	0.85[EUR][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	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7564719	EML6	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54805400-54830200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:54816200-54830600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:54822200-54833800	Genic enhancers	HepG2	liver
4	chr2:54822400-54833600	Enhancers	Psoas Muscle	Psoas
5	chr2:54822400-54833800	Enhancers	Stomach Mucosa	stomach
6	chr2:54822400-54834000	Enhancers	Right Atrium	heart
7	chr2:54822800-54831600	Genic enhancers	A549	lung
8	chr2:54823200-54831000	Genic enhancers	Fetal Intestine Large	intestine
9	chr2:54824200-54830600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:54824200-54833600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr2:54824600-54834400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:54824800-54834400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:54824800-54839200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:54825000-54829800	Weak transcription	Fetal Brain Male	brain
15	chr2:54826000-54831200	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr2:54826400-54830200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:54826600-54832000	Genic enhancers	Fetal Intestine Small	intestine
18	chr2:54826800-54830200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr2:54826800-54834400	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr2:54827200-54830000	Genic enhancers	Primary B cells from peripheral blood	blood
21	chr2:54827200-54830400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:54827200-54832200	Enhancers	Stomach Smooth Muscle	stomach
23	chr2:54827200-54833800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr2:54827200-54834000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:54827200-54839000	Weak transcription	Hela-S3	cervix
26	chr2:54827400-54830200	Weak transcription	Thymus	Thymus
27	chr2:54827400-54831000	Enhancers	Rectal Smooth Muscle	rectum
28	chr2:54827400-54832000	Weak transcription	Brain Germinal Matrix	brain
29	chr2:54827400-54832000	Weak transcription	Fetal Brain Female	brain
30	chr2:54827600-54830600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr2:54827600-54830600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:54827600-54830800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr2:54827600-54831200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:54827600-54831800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr2:54827600-54832200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr2:54827600-54833000	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr2:54827600-54834000	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr2:54827600-54834000	Enhancers	Right Ventricle	heart
39	chr2:54827600-54834400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:54827600-54834400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr2:54827600-54839200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:54827600-54839200	Weak transcription	Dnd41	blood
43	chr2:54827800-54830200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:54827800-54830200	Weak transcription	Aorta	Aorta
45	chr2:54827800-54830400	Enhancers	Liver	Liver
46	chr2:54827800-54831200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:54827800-54834000	Enhancers	Brain Anterior Caudate	brain
48	chr2:54827800-54834000	Enhancers	NHDF-Ad	bronchial
49	chr2:54827800-54835600	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr2:54828000-54829800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links