Variant report

Variant	rs6545430
Chromosome Location	chr2:54788276-54788277
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54767756..54770528-chr2:54788177..54790066,2	MCF-7	breast:
2	chr2:54786715..54789713-chr2:54890702..54893003,2	K562	blood:
3	chr2:54342378..54344218-chr2:54786110..54788365,2	MCF-7	breast:
4	chr2:54749132..54757147-chr2:54784492..54789269,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237887	Chromatin interaction
ENSG00000228108	Chromatin interaction
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10166844	0.85[ASN][1000 genomes]
rs10169439	0.90[CEU][hapmap]
rs10169954	0.81[ASN][1000 genomes]
rs10170066	0.83[ASN][1000 genomes]
rs10170355	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10176359	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs10176445	1.00[CHB][hapmap]
rs10182538	0.83[ASN][1000 genomes]
rs10182836	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10183043	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10183867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10184128	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10187338	0.83[ASN][1000 genomes]
rs10188185	1.00[CHB][hapmap]
rs10188545	0.84[ASN][1000 genomes]
rs10193692	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10205410	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs10206143	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10208225	0.83[ASN][1000 genomes]
rs10210502	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10528	0.92[CEU][hapmap];0.88[CHB][hapmap];0.83[EUR][1000 genomes]
rs1137645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11555856	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11892236	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs11892443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11896957	0.84[EUR][1000 genomes]
rs11898032	0.86[ASN][1000 genomes]
rs11898033	0.86[ASN][1000 genomes]
rs11902659	0.84[EUR][1000 genomes]
rs11902987	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11904679	0.85[CEU][hapmap];0.89[CHB][hapmap];0.81[EUR][1000 genomes]
rs12713262	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713263	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713264	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs12713265	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12713266	0.83[ASN][1000 genomes]
rs12713268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12713269	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12713270	0.88[EUR][1000 genomes]
rs12713271	0.88[EUR][1000 genomes]
rs12713272	0.84[EUR][1000 genomes]
rs12713273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12987967	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13021606	0.84[EUR][1000 genomes]
rs13021615	0.86[CEU][hapmap];0.88[CHB][hapmap];0.82[EUR][1000 genomes]
rs13386146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13391522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13391803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13399656	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13403284	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13407214	0.84[ASN][1000 genomes]
rs13423873	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13428703	0.85[CEU][hapmap]
rs13432302	0.83[ASN][1000 genomes]
rs17039558	0.92[CEU][hapmap];0.89[CHB][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17045939	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs17046061	0.82[EUR][1000 genomes]
rs17046067	0.82[EUR][1000 genomes]
rs17046077	0.86[CEU][hapmap];0.85[CHB][hapmap]
rs17046097	0.86[JPT][hapmap]
rs17046108	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs17046257	1.00[CHB][hapmap]
rs2048370	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2229503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs2271329	0.86[CEU][hapmap];0.88[CHB][hapmap]
rs28581481	0.81[ASN][1000 genomes]
rs3287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs34077590	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34094680	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34308676	0.85[EUR][1000 genomes]
rs34311770	0.82[EUR][1000 genomes]
rs34978408	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs354232	0.89[CHB][hapmap]
rs35619551	0.81[EUR][1000 genomes]
rs3739109	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3796017	0.83[ASN][1000 genomes]
rs3796018	0.83[ASN][1000 genomes]
rs3796019	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3796022	0.85[CEU][hapmap];0.89[CHB][hapmap];0.82[EUR][1000 genomes]
rs4261758	0.92[CEU][hapmap];0.89[CHB][hapmap];0.83[EUR][1000 genomes]
rs4319969	0.86[CEU][hapmap];0.89[CHB][hapmap]
rs4346422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4347868	0.83[ASN][1000 genomes]
rs4358162	0.88[EUR][1000 genomes]
rs4374410	0.87[ASN][1000 genomes]
rs4455200	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4519566	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4577321	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4616509	0.83[ASN][1000 genomes]
rs4641979	0.83[ASN][1000 genomes]
rs57281248	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58419243	0.82[EUR][1000 genomes]
rs61126015	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545435	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs66693131	0.82[EUR][1000 genomes]
rs6706263	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs67079536	0.85[EUR][1000 genomes]
rs6708082	0.85[CEU][hapmap]
rs6721612	0.84[EUR][1000 genomes]
rs6724136	0.85[EUR][1000 genomes]
rs67244067	0.86[EUR][1000 genomes]
rs6730876	0.84[EUR][1000 genomes]
rs6734445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6734536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6739140	0.86[ASN][1000 genomes]
rs6741053	0.81[EUR][1000 genomes]
rs6749802	0.86[ASN][1000 genomes]
rs6752720	0.85[CEU][hapmap]
rs7340302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7424459	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7556752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7564719	0.84[ASN][1000 genomes]
rs7569127	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs7584223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7586066	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7586311	0.83[ASN][1000 genomes]
rs7599241	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7602992	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7608414	1.00[CHB][hapmap]

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	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	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	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
rs6545430	EML6	cis	Thyroid	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54784200-54788400	Active TSS	H9 Cell Line	embryonic stem cell
2	chr2:54784400-54788400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:54784600-54788400	Active TSS	Thymus	Thymus
4	chr2:54784600-54788600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr2:54784600-54788800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:54784800-54788400	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr2:54784800-54788400	Active TSS	Fetal Intestine Small	intestine
8	chr2:54784800-54788400	Active TSS	Pancreas	Pancrea
9	chr2:54784800-54788600	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr2:54784800-54789000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:54784800-54789800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:54785000-54788400	Active TSS	Fetal Intestine Large	intestine
13	chr2:54785000-54788400	Active TSS	Hela-S3	cervix
14	chr2:54785000-54788600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:54785000-54788600	Active TSS	Stomach Mucosa	stomach
16	chr2:54785000-54789000	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr2:54785000-54789400	Active TSS	GM12878-XiMat	blood
18	chr2:54785400-54789000	Active TSS	HMEC	breast
19	chr2:54786400-54789000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:54786400-54790200	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr2:54786400-54793200	Enhancers	Fetal Heart	heart
22	chr2:54786600-54788400	Active TSS	Colonic Mucosa	Colon
23	chr2:54786600-54788800	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr2:54787200-54788400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:54787200-54788400	Enhancers	Fetal Brain Male	brain
26	chr2:54787200-54788400	Active TSS	Right Atrium	heart
27	chr2:54787200-54788800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:54787200-54788800	Active TSS	Rectal Smooth Muscle	rectum
29	chr2:54787200-54789800	Active TSS	Fetal Stomach	stomach
30	chr2:54787400-54788600	Flanking Active TSS	NHLF	lung
31	chr2:54787400-54788800	Flanking Active TSS	HUVEC	blood vessel
32	chr2:54787600-54788400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:54787600-54788400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr2:54787600-54788400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:54787600-54788600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr2:54787600-54788600	Enhancers	Brain Angular Gyrus	brain
37	chr2:54787600-54788600	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr2:54787600-54789000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:54787600-54789200	Weak transcription	Brain Substantia Nigra	brain
40	chr2:54787600-54791400	Enhancers	Left Ventricle	heart
41	chr2:54787600-54791400	Weak transcription	Right Ventricle	heart
42	chr2:54787600-54791400	Weak transcription	Spleen	Spleen
43	chr2:54787600-54796800	Weak transcription	Aorta	Aorta
44	chr2:54787600-54797000	Weak transcription	Gastric	stomach
45	chr2:54787800-54788400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr2:54787800-54788400	Active TSS	HSMM	muscle
47	chr2:54787800-54788400	Flanking Active TSS	Osteobl	bone
48	chr2:54787800-54788600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr2:54787800-54788600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:54787800-54788600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum

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