Variant report

Variant	rs6546039
Chromosome Location	chr2:64118877-64118878
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:64116985..64119241-chr2:64121510..64125671,3	K562	blood:
2	chr2:64101796..64104187-chr2:64117437..64118984,2	MCF-7	breast:
3	chr2:64115192..64117886-chr2:64118727..64121614,2	MCF-7	breast:
4	chr2:64067276..64069517-chr2:64115717..64120116,4	K562	blood:

Variant related genes	Relation type
ENSG00000169764	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10171008	0.85[ASN][1000 genomes]
rs10187013	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs10201844	0.89[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[GIH][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10207847	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10211360	0.89[CHB][hapmap]
rs11125985	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11125986	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12612549	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12612596	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12613707	0.85[EUR][1000 genomes]
rs12713497	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs13006124	0.84[CHB][hapmap]
rs13384707	0.95[CEU][hapmap];0.89[CHB][hapmap];0.84[EUR][1000 genomes]
rs1362797	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1440004	0.92[EUR][1000 genomes]
rs17619717	0.84[CHB][hapmap]
rs2054119	0.84[EUR][1000 genomes]
rs2080649	0.89[EUR][1000 genomes]
rs2165210	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2302809	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2901636	0.91[EUR][1000 genomes]
rs329477	0.91[EUR][1000 genomes]
rs329486	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs36042418	0.82[EUR][1000 genomes]
rs3980405	0.90[EUR][1000 genomes]
rs4072113	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4293553	1.00[ASW][hapmap]
rs4359637	0.84[EUR][1000 genomes]
rs4399712	0.83[EUR][1000 genomes]
rs4671528	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs4671532	0.81[EUR][1000 genomes]
rs6546025	0.95[CEU][hapmap];0.84[CHB][hapmap];0.85[YRI][hapmap]
rs6546026	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap]
rs6546027	0.83[EUR][1000 genomes]
rs6546038	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6546040	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6546042	0.80[ASN][1000 genomes]
rs6546043	0.82[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap]
rs6546046	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]
rs6705192	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6716322	0.91[EUR][1000 genomes]
rs6716558	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6724024	0.83[ASN][1000 genomes]
rs6726257	0.83[CHB][hapmap]
rs6727120	0.85[EUR][1000 genomes]
rs6737855	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6741298	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs6741584	0.89[CHB][hapmap]
rs6746875	0.92[EUR][1000 genomes]
rs6747307	0.89[CHB][hapmap]
rs6757168	0.86[ASN][1000 genomes]
rs7420396	0.85[ASN][1000 genomes]
rs7560265	0.80[ASN][1000 genomes]
rs7589241	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7596262	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7597935	0.84[CHB][hapmap]
rs7602952	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7608885	0.87[EUR][1000 genomes]
rs9309356	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs998043	0.82[EUR][1000 genomes]

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	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	nsv521717	chr2:64104132-64186582	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64083000-64123000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:64083000-64129200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:64103600-64128400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:64103800-64130400	Weak transcription	Stomach Mucosa	stomach
5	chr2:64105200-64121600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:64107200-64130000	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:64107400-64119000	Strong transcription	HSMMtube	muscle
8	chr2:64107400-64119200	Strong transcription	Primary B cells from cord blood	blood
9	chr2:64107400-64121400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:64107400-64121800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:64107400-64127600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr2:64107400-64129600	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr2:64107600-64122000	Strong transcription	HSMM	muscle
14	chr2:64107600-64122200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:64107600-64122200	Strong transcription	Primary B cells from peripheral blood	blood
16	chr2:64107600-64122200	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr2:64107600-64128800	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr2:64107600-64129200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:64107800-64124600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:64107800-64126200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:64107800-64127000	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr2:64108200-64120800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:64108200-64121800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:64108200-64127200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:64108400-64121400	Strong transcription	HMEC	breast
26	chr2:64108400-64127200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:64108600-64128200	Strong transcription	Primary hematopoietic stem cells	blood
28	chr2:64108800-64121400	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:64108800-64121400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:64108800-64121800	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr2:64109000-64122200	Strong transcription	NHDF-Ad	bronchial
32	chr2:64109200-64125800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr2:64109400-64119000	Strong transcription	Fetal Intestine Large	intestine
34	chr2:64109400-64119600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:64109400-64127000	Strong transcription	Placenta	Placenta
36	chr2:64109400-64129000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr2:64109600-64119600	Strong transcription	Thymus	Thymus
38	chr2:64109600-64119800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr2:64109600-64120600	Strong transcription	GM12878-XiMat	blood
40	chr2:64109600-64122800	Strong transcription	Fetal Muscle Trunk	muscle
41	chr2:64109600-64127000	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr2:64109600-64128400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:64109800-64121400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr2:64109800-64122800	Strong transcription	Osteobl	bone
45	chr2:64109800-64128600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:64110000-64119600	Strong transcription	NHLF	lung
47	chr2:64110000-64120000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr2:64110000-64120600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr2:64110000-64122000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr2:64110000-64126800	Strong transcription	Adipose Nuclei	Adipose

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