Variant report

Variant	rs6545429
Chromosome Location	chr2:54776127-54776128
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54770128..54773516-chr2:54775238..54777528,3	MCF-7	breast:
2	chr2:54767808..54771330-chr2:54771769..54776449,4	K562	blood:
3	chr2:54763693..54765544-chr2:54775882..54778958,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228108	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10165490	0.80[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs10180713	0.85[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1047499	0.85[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11885703	0.80[EUR][1000 genomes]
rs11892788	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11898012	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12104998	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12105792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12467581	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12468469	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12617036	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713260	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13016942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13399435	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1367295	1.00[CEU][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1541854	0.90[EUR][1000 genomes]
rs17344044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17344072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17521078	1.00[CEU][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1802889	0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs1864493	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2292356	0.85[EUR][1000 genomes]
rs2292357	0.81[EUR][1000 genomes]
rs2941583	0.81[AFR][1000 genomes]
rs2941586	0.85[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2941587	0.85[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2941595	0.85[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2971877	0.85[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2971879	0.85[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2971883	1.00[AFR][1000 genomes]
rs2971887	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs354231	0.83[CEU][hapmap]
rs3796014	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4233952	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4233954	0.85[EUR][1000 genomes]
rs4444573	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4455199	0.90[EUR][1000 genomes]
rs4514917	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4519562	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4592889	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671221	0.95[CEU][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671222	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671225	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4671226	0.95[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4671945	1.00[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671946	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4671947	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4671949	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671950	0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs4671951	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4671954	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671955	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4990319	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6545411	0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545413	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545414	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545415	0.90[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6545418	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6545419	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545427	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6545434	0.85[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6704769	0.95[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6706372	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs6724590	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6729826	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6731661	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs6732949	0.84[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6734658	0.90[EUR][1000 genomes]
rs6735813	0.89[EUR][1000 genomes]
rs6742607	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6746016	0.90[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6746306	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6748816	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6761369	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6761398	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7558950	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7563706	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7589236	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7607451	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs907135	0.80[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv528848	chr2:54758305-54777576	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	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
rs6545429	EML6	cis	Thyroid	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
3	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:54757000-54776800	Weak transcription	Brain Germinal Matrix	brain
5	chr2:54758200-54778200	Weak transcription	Placenta	Placenta
6	chr2:54764000-54776800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:54768200-54783800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:54769800-54777000	Weak transcription	Psoas Muscle	Psoas
9	chr2:54770000-54777400	Weak transcription	GM12878-XiMat	blood
10	chr2:54770400-54776800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:54770400-54782000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:54770600-54776800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:54770600-54780200	Enhancers	Fetal Intestine Large	intestine
14	chr2:54771600-54783400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:54772600-54778800	Enhancers	Brain Anterior Caudate	brain
16	chr2:54772600-54780200	Enhancers	Fetal Intestine Small	intestine
17	chr2:54773200-54777200	Weak transcription	NHLF	lung
18	chr2:54773400-54776800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:54773400-54784000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:54773400-54784000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:54773800-54776800	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:54773800-54777000	Weak transcription	Aorta	Aorta
23	chr2:54773800-54782200	Weak transcription	Ovary	ovary
24	chr2:54774000-54776800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:54774000-54776800	Weak transcription	Adipose Nuclei	Adipose
26	chr2:54774000-54776800	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr2:54774000-54777200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:54774000-54777400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:54774000-54779200	Enhancers	Duodenum Mucosa	Duodenum
30	chr2:54774000-54782400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:54774000-54782400	Weak transcription	Osteobl	bone
32	chr2:54774200-54776600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:54774200-54778000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr2:54774200-54778000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:54774200-54779800	Weak transcription	NHDF-Ad	bronchial
36	chr2:54774400-54777000	Strong transcription	Fetal Lung	lung
37	chr2:54774600-54776800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:54774600-54777000	Weak transcription	Fetal Kidney	kidney
39	chr2:54774600-54777800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr2:54774600-54778000	Enhancers	Fetal Brain Male	brain
41	chr2:54774800-54776600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:54774800-54776800	Weak transcription	HSMMtube	muscle
43	chr2:54774800-54778400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:54774800-54778800	Enhancers	Brain Hippocampus Middle	brain
45	chr2:54774800-54781800	Weak transcription	Liver	Liver
46	chr2:54774800-54782400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:54775200-54778000	Enhancers	Fetal Brain Female	brain
48	chr2:54775400-54776600	Enhancers	Fetal Heart	heart
49	chr2:54775400-54776800	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr2:54775400-54777000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links