Variant report

Variant	rs34978408
Chromosome Location	chr2:54791687-54791688
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54790164..54792599-chr2:54886849..54889331,2	K562	blood:
2	chr2:54789686..54792599-chr2:54886831..54888349,2	K562	blood:
3	chr2:54789909..54791873-chr2:54794483..54796038,2	MCF-7	breast:
4	chr2:54790537..54793498-chr2:54814882..54817196,2	MCF-7	breast:
5	chr2:54789199..54791941-chr2:54810651..54814148,3	K562	blood:

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10166844	0.82[ASN][1000 genomes]
rs10176359	0.82[EUR][1000 genomes]
rs10183043	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10184128	0.81[ASN][1000 genomes]
rs10188545	0.81[ASN][1000 genomes]
rs10205410	0.81[ASN][1000 genomes]
rs10210502	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10528	0.90[EUR][1000 genomes]
rs11555856	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11892236	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11896957	0.89[EUR][1000 genomes]
rs11898032	0.83[ASN][1000 genomes]
rs11898033	0.83[ASN][1000 genomes]
rs11902659	0.82[EUR][1000 genomes]
rs11904679	0.85[EUR][1000 genomes]
rs12713262	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713263	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713270	0.85[EUR][1000 genomes]
rs12713271	0.85[EUR][1000 genomes]
rs12713272	0.82[EUR][1000 genomes]
rs12713273	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12987967	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13004944	0.83[EUR][1000 genomes]
rs13006815	0.81[EUR][1000 genomes]
rs13021606	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13021615	0.92[EUR][1000 genomes]
rs13036147	0.84[EUR][1000 genomes]
rs13386146	0.81[ASN][1000 genomes]
rs13391803	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13399656	0.81[ASN][1000 genomes]
rs13407214	0.81[ASN][1000 genomes]
rs13423873	0.86[ASN][1000 genomes]
rs17039558	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17045939	0.84[EUR][1000 genomes]
rs17046036	0.83[EUR][1000 genomes]
rs17046061	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17046067	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17046077	0.83[EUR][1000 genomes]
rs17046108	0.84[EUR][1000 genomes]
rs2229503	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2271329	0.83[EUR][1000 genomes]
rs34077590	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34094680	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34263579	0.88[EUR][1000 genomes]
rs34308676	0.92[EUR][1000 genomes]
rs34311770	0.88[EUR][1000 genomes]
rs34429083	0.86[EUR][1000 genomes]
rs35619551	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36018286	0.86[EUR][1000 genomes]
rs3739109	0.82[EUR][1000 genomes]
rs3796022	0.86[EUR][1000 genomes]
rs4261758	0.89[EUR][1000 genomes]
rs4319969	0.84[EUR][1000 genomes]
rs4346422	0.81[ASN][1000 genomes]
rs4347868	0.83[ASN][1000 genomes]
rs4358162	0.85[EUR][1000 genomes]
rs4374410	0.84[ASN][1000 genomes]
rs4455200	0.81[ASN][1000 genomes]
rs4519566	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs45487791	0.86[EUR][1000 genomes]
rs4577321	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57281248	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58419243	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61126015	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6545430	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545435	0.87[EUR][1000 genomes]
rs66693131	0.86[EUR][1000 genomes]
rs67079536	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6721612	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6724136	0.85[EUR][1000 genomes]
rs67244067	0.84[EUR][1000 genomes]
rs6730876	0.89[EUR][1000 genomes]
rs6734445	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6734536	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6739140	0.83[ASN][1000 genomes]
rs6741053	0.85[EUR][1000 genomes]
rs6749802	0.83[ASN][1000 genomes]
rs72806653	0.84[EUR][1000 genomes]
rs7340302	0.81[ASN][1000 genomes]
rs7424459	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7564719	0.81[ASN][1000 genomes]
rs7569127	0.82[EUR][1000 genomes]
rs7584223	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7586066	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7599241	0.81[ASN][1000 genomes]
rs7602992	0.89[EUR][1000 genomes];0.82[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	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
rs34978408	EML6	cis	Thyroid	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54786400-54793200	Enhancers	Fetal Heart	heart
2	chr2:54787600-54796800	Weak transcription	Aorta	Aorta
3	chr2:54787600-54797000	Weak transcription	Gastric	stomach
4	chr2:54787800-54796200	Weak transcription	Esophagus	oesophagus
5	chr2:54787800-54797200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:54788000-54796000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:54788200-54795000	Weak transcription	Brain Anterior Caudate	brain
8	chr2:54788400-54797600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:54788600-54791800	Enhancers	Stomach Mucosa	stomach
10	chr2:54788600-54792000	Enhancers	Fetal Thymus	thymus
11	chr2:54788600-54795200	Weak transcription	Placenta	Placenta
12	chr2:54788600-54796000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:54788600-54796200	Weak transcription	Colonic Mucosa	Colon
14	chr2:54788600-54796200	Weak transcription	Fetal Muscle Leg	muscle
15	chr2:54788600-54796400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr2:54788600-54796800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:54788600-54796800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:54788800-54796000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:54789200-54796200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:54789400-54791800	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr2:54789400-54792000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:54789400-54792800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr2:54789400-54795800	Weak transcription	NHLF	lung
24	chr2:54789400-54796000	Weak transcription	Brain Hippocampus Middle	brain
25	chr2:54789400-54796000	Weak transcription	HSMMtube	muscle
26	chr2:54789400-54796200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:54789400-54796200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:54789400-54796400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:54789600-54792400	Weak transcription	HUVEC	blood vessel
30	chr2:54789600-54792800	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr2:54789600-54795200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr2:54789600-54795800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:54789600-54795800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr2:54789600-54795800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr2:54789600-54795800	Weak transcription	NH-A	brain
36	chr2:54789600-54796000	Weak transcription	Brain Angular Gyrus	brain
37	chr2:54789600-54796000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr2:54789600-54796000	Weak transcription	Brain Substantia Nigra	brain
39	chr2:54789600-54796000	Weak transcription	HMEC	breast
40	chr2:54789600-54796000	Weak transcription	HSMM	muscle
41	chr2:54789600-54796000	Weak transcription	NHDF-Ad	bronchial
42	chr2:54789600-54796000	Weak transcription	Osteobl	bone
43	chr2:54789600-54796200	Enhancers	Primary B cells from peripheral blood	blood
44	chr2:54789600-54796800	Weak transcription	Psoas Muscle	Psoas
45	chr2:54789800-54795000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:54789800-54795200	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr2:54789800-54795800	Weak transcription	NHEK	skin
48	chr2:54789800-54796000	Enhancers	Primary T cells fromperipheralblood	blood
49	chr2:54789800-54801400	Enhancers	Liver	Liver
50	chr2:54790000-54792000	Transcr. at gene 5' and 3'	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links