Variant report

Variant	rs2842519
Chromosome Location	chr6:37934269-37934270
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: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11963886	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496579	1.00[ASW][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890244	1.00[CEU][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890367	0.90[ASW][hapmap];1.00[CEU][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2495213	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645103	1.00[ASN][1000 genomes]
rs2645119	1.00[MEX][hapmap]
rs2645129	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2645133	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645135	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645136	1.00[ASN][1000 genomes]
rs2645138	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2749920	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2842501	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842502	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2842504	1.00[ASN][1000 genomes]
rs2842509	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842518	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs6458033	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs6930917	1.00[CEU][hapmap];0.94[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7765420	1.00[ASN][1000 genomes]
rs7775465	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380711	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:69 , 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	chr6:37924600-37941600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:37925000-37934600	Weak transcription	A549	lung
13	chr6:37925200-37938800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr6:37925400-37939400	Weak transcription	Adipose Nuclei	Adipose
15	chr6:37925600-37936400	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:37926000-37936200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:37926800-37955000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:37927000-37937600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:37927000-37942400	Weak transcription	Psoas Muscle	Psoas
20	chr6:37927200-37942400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:37928000-37934400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:37928000-37935800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr6:37929400-37936200	Weak transcription	Left Ventricle	heart
24	chr6:37929400-37938200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr6:37929400-37938800	Weak transcription	Fetal Stomach	stomach
26	chr6:37929400-37939400	Weak transcription	Spleen	Spleen
27	chr6:37929400-37942000	Weak transcription	Esophagus	oesophagus
28	chr6:37929400-37947800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:37929400-37953200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:37930200-37941600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:37930200-37942200	Weak transcription	HepG2	liver
32	chr6:37930400-37938200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr6:37930400-37939400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr6:37930600-37934600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:37930600-37941800	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr6:37930800-37939200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr6:37931000-37934400	Weak transcription	Primary T cells from cord blood	blood
38	chr6:37931000-37934600	Weak transcription	Thymus	Thymus
39	chr6:37931000-37939000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr6:37931000-37939400	Weak transcription	Fetal Thymus	thymus
41	chr6:37932000-37934800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr6:37932200-37936800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr6:37933000-37935200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:37933200-37934400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:37933200-37934400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:37933200-37934600	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr6:37933200-37934800	Enhancers	HUVEC	blood vessel
48	chr6:37933200-37934800	Enhancers	Osteobl	bone
49	chr6:37933200-37935000	Enhancers	NHDF-Ad	bronchial
50	chr6:37933200-37935200	Enhancers	NHEK	skin

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