Variant report

Variant	rs6545513
Chromosome Location	chr2:55884864-55884865
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55884125..55886913-chr2:55887602..55890288,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10172181	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10172506	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10173150	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10182131	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10194634	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs10195281	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10200159	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10203953	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10204169	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10208774	0.83[YRI][hapmap]
rs10221888	0.90[YRI][hapmap]
rs10427222	0.93[YRI][hapmap]
rs1045920	0.89[AMR][1000 genomes]
rs10496044	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11676573	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs11900763	0.93[YRI][hapmap]
rs11902712	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12615063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12616502	1.00[CHB][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs12616982	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12622830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12623625	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12989898	0.83[YRI][hapmap]
rs13028892	0.93[YRI][hapmap]
rs13382187	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13383352	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13399762	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13400946	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13403782	0.90[AFR][1000 genomes]
rs13407344	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13420929	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13428382	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13428486	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13430684	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17047094	1.00[CHB][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17047119	1.00[CHB][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2867964	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3748945	0.83[YRI][hapmap]
rs3748955	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3816489	0.93[YRI][hapmap]
rs4671248	0.81[LWK][hapmap];0.93[YRI][hapmap]
rs6545507	0.89[ASN][1000 genomes]
rs6545508	0.80[ASW][hapmap];1.00[CHD][hapmap];0.96[YRI][hapmap];0.89[ASN][1000 genomes]
rs6545509	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6545510	1.00[CHB][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6545512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6705295	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6712314	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6716100	0.86[YRI][hapmap]
rs6717574	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs6725101	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6736996	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6739788	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6745430	0.83[ASN][1000 genomes]
rs6745650	0.82[YRI][hapmap]
rs6760959	1.00[CHB][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs736345	1.00[CHB][hapmap];0.85[YRI][hapmap];0.83[ASN][1000 genomes]
rs744514	0.82[YRI][hapmap]
rs7558127	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7567115	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7571482	0.87[AFR][1000 genomes]
rs7575906	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7582174	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7584120	0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs7586115	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7586124	0.80[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7586366	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7594212	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7594497	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9309267	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9309268	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9636439	0.93[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:55847600-55886600	Weak transcription	Stomach Mucosa	stomach
4	chr2:55858200-55920400	Weak transcription	Fetal Heart	heart
5	chr2:55860400-55905400	Weak transcription	Fetal Brain Male	brain
6	chr2:55864000-55893200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:55864400-55919600	Weak transcription	NHLF	lung
8	chr2:55866600-55920000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:55870400-55887600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:55870400-55887800	Weak transcription	Fetal Brain Female	brain
11	chr2:55870400-55920000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:55870600-55892800	Weak transcription	Psoas Muscle	Psoas
13	chr2:55870600-55920000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:55870800-55888000	Weak transcription	Colonic Mucosa	Colon
15	chr2:55870800-55893400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:55870800-55903600	Weak transcription	Gastric	stomach
17	chr2:55870800-55909000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:55870800-55920400	Weak transcription	Aorta	Aorta
19	chr2:55871000-55887800	Weak transcription	Esophagus	oesophagus
20	chr2:55871000-55893200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:55871000-55893200	Weak transcription	Thymus	Thymus
22	chr2:55871000-55920000	Weak transcription	Spleen	Spleen
23	chr2:55871200-55893400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:55871200-55905200	Weak transcription	Brain Angular Gyrus	brain
25	chr2:55871400-55905200	Weak transcription	Fetal Kidney	kidney
26	chr2:55873000-55888400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr2:55873200-55893200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:55873200-55919800	Weak transcription	Small Intestine	intestine
29	chr2:55873800-55899400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr2:55874800-55920200	Weak transcription	Pancreas	Pancrea
31	chr2:55875600-55887200	Weak transcription	K562	blood
32	chr2:55879000-55888800	Strong transcription	Liver	Liver
33	chr2:55879000-55889000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:55879000-55890400	Strong transcription	Fetal Muscle Leg	muscle
35	chr2:55879000-55891800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:55879000-55896200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:55879000-55917600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:55879200-55886600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr2:55879200-55889800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:55879200-55902800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:55879400-55914200	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr2:55879600-55891800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:55880000-55887800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr2:55880400-55889600	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr2:55880400-55890800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:55880600-55885200	Strong transcription	GM12878-XiMat	blood
47	chr2:55881200-55913000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr2:55881800-55887800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr2:55881800-55898000	Weak transcription	NHDF-Ad	bronchial
50	chr2:55882000-55887600	Weak transcription	Lung	lung

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