Variant report

Variant	rs6544908
Chromosome Location	chr2:46868682-46868683
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46867409..46869384-chr2:46873725..46875843,2	MCF-7	breast:
2	chr2:46867092..46870472-chr2:46872248..46874879,4	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1057899	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1060656	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs11306	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1137748	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs11901678	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13404342	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs13406609	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs13410076	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1376406	0.85[ASN][1000 genomes]
rs1456018	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17035361	0.85[ASN][1000 genomes]
rs1809087	0.82[CHB][hapmap]
rs2276554	0.82[ASN][1000 genomes]
rs3213985	1.00[CEU][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3768723	0.85[ASN][1000 genomes]
rs3768724	0.94[EUR][1000 genomes]
rs3768725	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs3814042	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4300884	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4377377	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57134465	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57955462	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58101879	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58342271	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59183773	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60211996	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60738814	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61252474	0.85[ASN][1000 genomes]
rs6544904	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6713104	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6719813	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs6727471	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6733143	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6756134	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs7563577	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7589908	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7592446	0.91[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	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
9	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46844800-46868800	Weak transcription	Esophagus	oesophagus
2	chr2:46844800-46872200	Weak transcription	Pancreas	Pancrea
3	chr2:46845400-46871000	Weak transcription	Stomach Mucosa	stomach
4	chr2:46845400-46873000	Weak transcription	Right Ventricle	heart
5	chr2:46845600-46868800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:46848600-46871200	Weak transcription	HSMMtube	muscle
7	chr2:46848600-46872600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:46848600-46872800	Weak transcription	Left Ventricle	heart
9	chr2:46848600-46872800	Weak transcription	Ovary	ovary
10	chr2:46848800-46871000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:46848800-46872600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:46848800-46873000	Weak transcription	Brain Angular Gyrus	brain
13	chr2:46849000-46877200	Weak transcription	Brain Substantia Nigra	brain
14	chr2:46849200-46869400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:46849200-46869800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr2:46849200-46870800	Weak transcription	Hela-S3	cervix
17	chr2:46849200-46872600	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:46849400-46872800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:46852000-46872800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr2:46852400-46869400	Weak transcription	Dnd41	blood
21	chr2:46853400-46869600	Weak transcription	Brain Germinal Matrix	brain
22	chr2:46853400-46872600	Weak transcription	Brain Anterior Caudate	brain
23	chr2:46853400-46872800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr2:46853600-46869400	Weak transcription	NH-A	brain
25	chr2:46853800-46868800	Weak transcription	Placenta	Placenta
26	chr2:46853800-46873000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:46854400-46871800	Weak transcription	Fetal Lung	lung
28	chr2:46854600-46869000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:46854600-46869200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr2:46854800-46872800	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:46854800-46878600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr2:46856000-46868800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:46857200-46871800	Weak transcription	Adipose Nuclei	Adipose
34	chr2:46858000-46874800	Weak transcription	Liver	Liver
35	chr2:46858400-46869400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:46858600-46869200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr2:46859400-46868800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:46860400-46871000	Weak transcription	NHDF-Ad	bronchial
39	chr2:46862000-46868800	Weak transcription	GM12878-XiMat	blood
40	chr2:46862400-46869400	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr2:46862400-46877000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr2:46862600-46869000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:46862800-46869400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr2:46863000-46869400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:46865600-46869000	Weak transcription	A549	lung
46	chr2:46866800-46871000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr2:46867200-46869200	Weak transcription	Primary T cells from cord blood	blood
48	chr2:46867600-46872800	Weak transcription	Lung	lung
49	chr2:46868000-46868800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:46868000-46869800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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