Variant report

Variant	rs6545411
Chromosome Location	chr2:54727654-54727655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54340022..54344058-chr2:54726690..54729314,3	MCF-7	breast:
2	chr2:54727594..54730058-chr2:54731900..54733434,2	K562	blood:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10165490	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs1047499	0.89[TSI][hapmap]
rs11892788	0.90[CHB][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11898012	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.83[ASN][1000 genomes]
rs12104998	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12105792	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12467581	0.81[EUR][1000 genomes]
rs12468469	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12617036	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12713260	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13016942	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13399435	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs1367295	0.86[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1541854	0.82[EUR][1000 genomes]
rs17344044	0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs17344072	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17521078	0.86[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1802889	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs1864493	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2941595	0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs2971877	0.89[TSI][hapmap]
rs2971879	0.94[TSI][hapmap]
rs4233952	0.96[EUR][1000 genomes]
rs4444573	0.81[EUR][1000 genomes]
rs4455199	0.82[EUR][1000 genomes]
rs4514917	0.81[AMR][1000 genomes]
rs4519562	0.81[EUR][1000 genomes]
rs4592889	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4671221	0.85[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4671222	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4671225	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671226	0.91[CEU][hapmap];0.81[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4671945	0.86[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4671946	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4671947	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4671949	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4671950	0.86[CHB][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap]
rs4671951	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671954	0.82[ASN][1000 genomes]
rs4671955	0.83[EUR][1000 genomes]
rs4671956	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671960	0.81[TSI][hapmap]
rs4671961	0.81[TSI][hapmap]
rs4990319	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6545413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6545414	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6545415	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545418	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545419	0.91[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545427	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545429	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]
rs6545434	0.82[EUR][1000 genomes]
rs6704769	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs6706372	0.82[EUR][1000 genomes]
rs6724590	0.86[EUR][1000 genomes]
rs6729826	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6731661	0.81[EUR][1000 genomes]
rs6732949	0.81[EUR][1000 genomes]
rs6734658	0.82[EUR][1000 genomes]
rs6735813	0.80[EUR][1000 genomes]
rs6742607	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6746016	0.86[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6746306	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6748816	0.81[EUR][1000 genomes]
rs6761369	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6761398	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7558950	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7563706	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7589236	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7607451	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874150	chr2:54684557-54755229	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	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
4	nsv1002611	chr2:54718022-54752839	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv518406	chr2:54723271-54761329	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6545411	EML6	cis	Thyroid	GTEx
rs6545411	SPTBN1	cis	multi-tissue	Pritchard

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54710800-54729600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr2:54712400-54727800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:54712400-54729400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:54712400-54737000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:54712600-54727800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:54715600-54728200	Weak transcription	Brain Germinal Matrix	brain
7	chr2:54716000-54730000	Weak transcription	NH-A	brain
8	chr2:54716200-54728600	Weak transcription	Fetal Brain Female	brain
9	chr2:54717000-54729800	Weak transcription	Fetal Brain Male	brain
10	chr2:54717800-54732800	Enhancers	Brain Anterior Caudate	brain
11	chr2:54719000-54751800	Weak transcription	Aorta	Aorta
12	chr2:54719800-54728000	Weak transcription	Fetal Intestine Small	intestine
13	chr2:54719800-54728200	Weak transcription	Gastric	stomach
14	chr2:54722600-54728200	Weak transcription	Spleen	Spleen
15	chr2:54723800-54732600	Enhancers	Fetal Heart	heart
16	chr2:54723800-54733000	Enhancers	Adipose Nuclei	Adipose
17	chr2:54724000-54728600	Enhancers	HepG2	liver
18	chr2:54724000-54731400	Enhancers	Colon Smooth Muscle	Colon
19	chr2:54724200-54729600	Enhancers	Fetal Muscle Leg	muscle
20	chr2:54724200-54732800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:54724200-54732800	Enhancers	Brain Cingulate Gyrus	brain
22	chr2:54724400-54732800	Enhancers	Brain Hippocampus Middle	brain
23	chr2:54724600-54732800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:54724800-54728600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:54724800-54731400	Enhancers	Brain Substantia Nigra	brain
26	chr2:54724800-54732200	Enhancers	Ovary	ovary
27	chr2:54725000-54727800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:54725000-54733000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:54725200-54732200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr2:54725200-54737600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:54725400-54728200	Enhancers	HSMMtube	muscle
32	chr2:54725400-54729600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:54725400-54729800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr2:54725400-54730000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:54725600-54730000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr2:54725600-54730000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:54725600-54732600	Weak transcription	Small Intestine	intestine
38	chr2:54725800-54730000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:54725800-54731400	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr2:54725800-54732800	Enhancers	NHDF-Ad	bronchial
41	chr2:54726000-54728600	Enhancers	Stomach Smooth Muscle	stomach
42	chr2:54726000-54728800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr2:54726000-54733000	Enhancers	Brain Angular Gyrus	brain
44	chr2:54726200-54728000	Weak transcription	Stomach Mucosa	stomach
45	chr2:54726200-54729000	Enhancers	NHLF	lung
46	chr2:54726200-54729600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:54726200-54729800	Weak transcription	Fetal Thymus	thymus
48	chr2:54726200-54731800	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr2:54726400-54727800	Weak transcription	Lung	lung
50	chr2:54726400-54727800	Weak transcription	Right Atrium	heart

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