Variant report

Variant	rs6546046
Chromosome Location	chr2:64231079-64231080
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:64225373..64227940-chr2:64228601..64231174,2	K562	blood:
2	chr2:64230028..64232949-chr2:64243748..64246264,2	MCF-7	breast:
3	chr2:64227637..64233066-chr2:64233431..64237218,6	K562	blood:

Variant related genes	Relation type
ENSG00000143952	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10171008	0.92[ASN][1000 genomes]
rs10187013	0.94[CEU][hapmap]
rs10201844	0.95[CEU][hapmap];0.84[CHB][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap]
rs10207847	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10865343	0.84[CHB][hapmap]
rs11125986	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12464534	0.81[ASN][1000 genomes]
rs12611543	0.98[ASN][1000 genomes]
rs12612549	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs12615049	0.98[ASN][1000 genomes]
rs12988868	0.80[ASN][1000 genomes]
rs1362797	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1440004	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2080649	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2164735	0.80[ASN][1000 genomes]
rs2165210	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2302809	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2901636	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs329477	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs329480	0.84[CHB][hapmap]
rs329483	0.80[ASN][1000 genomes]
rs329486	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs329487	0.82[AMR][1000 genomes]
rs3980405	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4072113	0.95[CEU][hapmap];0.89[CHB][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap]
rs4293553	0.81[MKK][hapmap]
rs4318375	0.85[CHB][hapmap]
rs6546038	0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs6546039	0.95[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs6546040	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6546042	0.82[ASN][1000 genomes]
rs6546043	0.90[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs6705192	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6716322	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6716558	0.83[EUR][1000 genomes]
rs6724024	0.94[ASN][1000 genomes]
rs6727120	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6736556	0.82[ASN][1000 genomes]
rs6737855	0.95[CEU][hapmap];0.84[CHB][hapmap]
rs6746875	0.92[EUR][1000 genomes]
rs6755041	0.81[ASN][1000 genomes]
rs6757168	0.93[ASN][1000 genomes]
rs7420396	0.92[ASN][1000 genomes]
rs7560265	0.82[ASN][1000 genomes]
rs7589241	0.95[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7596262	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7602952	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7608885	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[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	nsv1013375	chr2:63969820-64231550	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002209	chr2:64160385-64238475	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv2763643	chr2:64219887-64281337	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64154800-64242600	Weak transcription	Aorta	Aorta
2	chr2:64185800-64245000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:64194000-64243200	Weak transcription	NHLF	lung
4	chr2:64202800-64232400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:64209400-64244800	Weak transcription	HSMM	muscle
6	chr2:64210200-64243000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr2:64213800-64244600	Weak transcription	HUVEC	blood vessel
8	chr2:64219200-64237000	Weak transcription	Placenta	Placenta
9	chr2:64219400-64238400	Weak transcription	Gastric	stomach
10	chr2:64222400-64242600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:64222400-64243000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:64223600-64235600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:64224800-64232600	Weak transcription	A549	lung
14	chr2:64224800-64233000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:64225400-64242200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr2:64225800-64237000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:64225800-64242600	Weak transcription	Fetal Kidney	kidney
18	chr2:64226000-64243000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:64226000-64245000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr2:64226200-64231400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr2:64226200-64245000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:64226200-64245000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:64226600-64242400	Weak transcription	Primary B cells from cord blood	blood
24	chr2:64226600-64242400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:64226800-64242600	Weak transcription	Small Intestine	intestine
26	chr2:64227000-64244600	Weak transcription	Fetal Brain Female	brain
27	chr2:64227200-64242000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr2:64227200-64245400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:64227400-64235600	Weak transcription	Fetal Thymus	thymus
30	chr2:64227800-64232600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:64228200-64239800	Weak transcription	Adipose Nuclei	Adipose
32	chr2:64228200-64243800	Weak transcription	Fetal Muscle Leg	muscle
33	chr2:64228400-64232000	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:64228600-64242600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:64228600-64243800	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr2:64228800-64232600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr2:64228800-64239200	Weak transcription	Fetal Lung	lung
38	chr2:64228800-64242600	Weak transcription	Dnd41	blood
39	chr2:64229000-64242000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:64229000-64244800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:64229000-64245000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:64229200-64231400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:64229200-64232800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr2:64229200-64242400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:64229200-64242600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:64229200-64243000	Weak transcription	Thymus	Thymus
47	chr2:64229200-64243800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:64229200-64244800	Weak transcription	Fetal Intestine Small	intestine
49	chr2:64229400-64234000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:64229400-64235200	Weak transcription	Left Ventricle	heart

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