Variant report

Variant	rs11898012
Chromosome Location	chr2:54777576-54777577
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr2:54777290-54777585	MCF-7	breast:	n/a	n/a
2	GATA3	chr2:54777290-54777594	T-47D	breast:	n/a	n/a
3	GATA3	chr2:54777231-54777680	T-47D	breast:	n/a	n/a
4	GATA2	chr2:54777270-54777690	SH-SY5Y	brain:	n/a	n/a
5	NR3C1	chr2:54777307-54777742	A549	lung:	n/a	chr2:54777556-54777570 chr2:54777675-54777682 chr2:54777552-54777573
6	GATA3	chr2:54777239-54777924	MCF-7	breast:	n/a	chr2:54777714-54777721 chr2:54777714-54777721 chr2:54777714-54777721 chr2:54777707-54777728

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54777010..54778863-chr2:54780329..54781851,2	MCF-7	breast:
2	chr2:54763693..54765544-chr2:54775882..54778958,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234943	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10165490	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10180713	1.00[YRI][hapmap]
rs1047499	0.83[TSI][hapmap];1.00[YRI][hapmap]
rs11892788	0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs12104998	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12105792	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12617036	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13016942	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13399435	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1367295	0.80[CHB][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs1510611	0.84[GIH][hapmap]
rs17344044	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17344072	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17521078	0.95[JPT][hapmap];0.91[TSI][hapmap];0.83[ASN][1000 genomes]
rs1802889	0.92[CEU][hapmap];0.85[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1864493	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2941586	1.00[YRI][hapmap]
rs2941587	1.00[YRI][hapmap]
rs2941595	0.88[TSI][hapmap];1.00[YRI][hapmap]
rs2971877	0.83[TSI][hapmap];1.00[YRI][hapmap]
rs2971879	0.88[TSI][hapmap];1.00[YRI][hapmap]
rs354236	0.86[TSI][hapmap]
rs4233954	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4514918	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4592889	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671221	0.82[CEU][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.83[ASN][1000 genomes]
rs4671222	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4671225	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671226	0.85[CHB][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs4671945	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4671946	0.82[EUR][1000 genomes]
rs4671947	0.82[EUR][1000 genomes]
rs4671949	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671950	0.96[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs4671951	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671953	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4671954	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671955	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4671956	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4671960	0.87[CEU][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs4671961	0.87[CEU][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs4990319	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6545411	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.83[ASN][1000 genomes]
rs6545413	0.84[ASN][1000 genomes]
rs6545414	0.84[ASN][1000 genomes]
rs6545415	0.81[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap]
rs6545418	0.81[ASN][1000 genomes]
rs6545419	0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs6545420	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6545421	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6545427	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6545429	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6545434	1.00[YRI][hapmap]
rs6704769	0.80[CHB][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs6729826	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6732949	1.00[YRI][hapmap]
rs6746016	1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs6746306	0.80[ASN][1000 genomes]
rs6761369	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6761398	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7558950	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7563706	0.82[ASN][1000 genomes]
rs7589236	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][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
rs11898012	EML6	cis	Thyroid	GTEx

Chromatin state (count:85 , 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	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:54758200-54778200	Weak transcription	Placenta	Placenta
4	chr2:54768200-54783800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:54770400-54782000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:54770600-54780200	Enhancers	Fetal Intestine Large	intestine
7	chr2:54771600-54783400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:54772600-54778800	Enhancers	Brain Anterior Caudate	brain
9	chr2:54772600-54780200	Enhancers	Fetal Intestine Small	intestine
10	chr2:54773400-54784000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:54773400-54784000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:54773800-54782200	Weak transcription	Ovary	ovary
13	chr2:54774000-54779200	Enhancers	Duodenum Mucosa	Duodenum
14	chr2:54774000-54782400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:54774000-54782400	Weak transcription	Osteobl	bone
16	chr2:54774200-54778000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr2:54774200-54778000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr2:54774200-54779800	Weak transcription	NHDF-Ad	bronchial
19	chr2:54774600-54777800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:54774600-54778000	Enhancers	Fetal Brain Male	brain
21	chr2:54774800-54778400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:54774800-54778800	Enhancers	Brain Hippocampus Middle	brain
23	chr2:54774800-54781800	Weak transcription	Liver	Liver
24	chr2:54774800-54782400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:54775200-54778000	Enhancers	Fetal Brain Female	brain
26	chr2:54775400-54777800	Enhancers	Gastric	stomach
27	chr2:54775400-54778600	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr2:54775400-54778800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:54775400-54778800	Enhancers	Right Atrium	heart
30	chr2:54775400-54778800	Enhancers	Right Ventricle	heart
31	chr2:54775400-54778800	Enhancers	Small Intestine	intestine
32	chr2:54775400-54778800	Enhancers	Stomach Mucosa	stomach
33	chr2:54775400-54778800	Enhancers	HMEC	breast
34	chr2:54775400-54779000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:54775400-54779200	Genic enhancers	HepG2	liver
36	chr2:54775600-54779400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:54775800-54777600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:54775800-54778000	Weak transcription	Spleen	Spleen
39	chr2:54775800-54778600	Enhancers	Brain Angular Gyrus	brain
40	chr2:54775800-54780600	Enhancers	Placenta Amnion	Placenta Amnion
41	chr2:54775800-54782400	Weak transcription	HSMM	muscle
42	chr2:54776000-54777800	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr2:54776000-54778200	Enhancers	Left Ventricle	heart
44	chr2:54776200-54778000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:54776600-54778600	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr2:54776600-54778800	Enhancers	Brain Cingulate Gyrus	brain
47	chr2:54776600-54778800	Enhancers	NHEK	skin
48	chr2:54776800-54777600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:54776800-54777600	Enhancers	Brain Germinal Matrix	brain
50	chr2:54776800-54777600	Enhancers	Colon Smooth Muscle	Colon

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