Variant report

Variant	rs2645107
Chromosome Location	chr6:37933881-37933882
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	chr6:37923129..37926098-chr6:37932741..37935067,3	MCF-7	breast:
2	chr6:37927855..37929395-chr6:37932120..37934567,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10456096	0.89[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap]
rs10456097	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10947713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1187421	0.82[CEU][hapmap];0.89[CHB][hapmap]
rs1187422	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1187423	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190570	0.89[CHB][hapmap]
rs12192182	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12194618	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12198907	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12200258	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12206818	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211981	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213151	0.81[EUR][1000 genomes]
rs12213835	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214375	0.92[CEU][hapmap]
rs13210701	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13214465	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13220131	0.87[EUR][1000 genomes]
rs16890277	0.81[ASN][1000 genomes]
rs16890344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs171831	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1812599	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2055206	0.81[CEU][hapmap]
rs2132597	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs259673	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259679	0.89[CHB][hapmap]
rs259684	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs259686	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259689	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259690	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259691	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259695	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259713	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259715	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259716	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs259718	0.89[CHB][hapmap]
rs2645102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2645113	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2645116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2645117	0.89[CHB][hapmap]
rs2645120	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2645124	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs2645127	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2645128	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2645131	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs2645134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2645137	0.82[EUR][1000 genomes]
rs2842500	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2842517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2842529	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2842531	0.81[YRI][hapmap]
rs34871463	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35823566	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56098839	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6458029	0.96[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap]
rs7747130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9296232	0.96[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap]
rs9394460	0.96[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap]
rs9647619	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966705	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1018711	chr6:37813397-37981590	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv602956	chr6:37909084-37986489	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2761037	chr6:37930659-37966762	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37911600-37935400	Weak transcription	Primary B cells from cord blood	blood
2	chr6:37911600-37936200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr6:37922600-37939000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr6:37922800-37938600	Weak transcription	Fetal Lung	lung
5	chr6:37922800-37957600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:37922800-37958600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:37923000-37939000	Weak transcription	Ovary	ovary
8	chr6:37923600-37938800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr6:37923600-37942200	Weak transcription	Aorta	Aorta
10	chr6:37923600-37947400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:37923800-37934200	Weak transcription	Fetal Muscle Leg	muscle
12	chr6:37924600-37941600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:37925000-37934600	Weak transcription	A549	lung
14	chr6:37925200-37938800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:37925400-37939400	Weak transcription	Adipose Nuclei	Adipose
16	chr6:37925600-37934200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:37925600-37936400	Weak transcription	Colon Smooth Muscle	Colon
18	chr6:37926000-37936200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:37926800-37955000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:37927000-37937600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:37927000-37942400	Weak transcription	Psoas Muscle	Psoas
22	chr6:37927200-37942400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr6:37928000-37934400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:37928000-37935800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr6:37929400-37936200	Weak transcription	Left Ventricle	heart
26	chr6:37929400-37938200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr6:37929400-37938800	Weak transcription	Fetal Stomach	stomach
28	chr6:37929400-37939400	Weak transcription	Spleen	Spleen
29	chr6:37929400-37942000	Weak transcription	Esophagus	oesophagus
30	chr6:37929400-37947800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:37929400-37953200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:37930200-37941600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:37930200-37942200	Weak transcription	HepG2	liver
34	chr6:37930400-37938200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr6:37930400-37939400	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr6:37930600-37934600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:37930600-37941800	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr6:37930800-37939200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr6:37931000-37934400	Weak transcription	Primary T cells from cord blood	blood
40	chr6:37931000-37934600	Weak transcription	Thymus	Thymus
41	chr6:37931000-37939000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:37931000-37939400	Weak transcription	Fetal Thymus	thymus
43	chr6:37932000-37934200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:37932000-37934800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr6:37932200-37936800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr6:37933000-37935200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:37933200-37934200	Enhancers	Stomach Mucosa	stomach
48	chr6:37933200-37934400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:37933200-37934400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:37933200-37934600	Enhancers	Pancreatic Islets	Pancreatic Islet

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