Variant report

Variant	rs3768730
Chromosome Location	chr2:46592524-46592525
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:46591157..46594128-chr2:46607853..46610004,2	MCF-7	breast:
2	chr2:46220243..46221278-chr2:46591939..46593140,4	K562	blood:
3	chr2:46484642..46486699-chr2:46592173..46593939,2	K562	blood:
4	chr2:46524982..46525947-chr2:46591731..46592823,3	MCF-7	breast:
5	chr2:46457086..46457764-chr2:46591788..46592693,3	MCF-7	breast:
6	chr2:46560872..46561764-chr2:46591768..46592627,2	MCF-7	breast:
7	chr2:46457257..46457931-chr2:46592203..46593157,2	MCF-7	breast:
8	chr2:46586164..46589641-chr2:46590092..46593590,4	K562	blood:
9	chr2:46591734..46592648-chr2:46688138..46688776,3	MCF-7	breast:
10	chr2:46590893..46592901-chr2:46596143..46597852,2	K562	blood:
11	chr2:46237825..46238545-chr2:46592073..46593003,2	MCF-7	breast:
12	chr2:46237747..46238657-chr2:46591753..46592698,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000116016	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10178633	0.81[CEU][hapmap]
rs10191091	0.89[MEX][hapmap]
rs11675232	0.92[CEU][hapmap]
rs11675441	0.88[CEU][hapmap]
rs11678465	0.89[CEU][hapmap]
rs11692911	0.92[CEU][hapmap]
rs11694193	0.89[CEU][hapmap]
rs12467821	0.81[CEU][hapmap]
rs12986653	1.00[YRI][hapmap]
rs13002880	1.00[YRI][hapmap]
rs13006131	0.85[CEU][hapmap]
rs13007688	1.00[YRI][hapmap]
rs13011481	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs13019268	0.85[MEX][hapmap]
rs13030579	1.00[YRI][hapmap]
rs1530621	1.00[YRI][hapmap]
rs1530631	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1530633	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1562452	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs1562453	0.81[CEU][hapmap]
rs2121698	1.00[YRI][hapmap]
rs2881324	0.85[CHB][hapmap];0.83[MEX][hapmap]
rs3754556	0.82[YRI][hapmap]
rs4952831	0.82[YRI][hapmap]
rs4952833	0.82[YRI][hapmap]
rs4953356	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs4953358	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs4953359	0.88[CEU][hapmap]
rs4953372	1.00[YRI][hapmap]
rs4953387	1.00[YRI][hapmap]
rs4953388	1.00[YRI][hapmap]
rs4953390	1.00[YRI][hapmap]
rs6544887	0.81[CEU][hapmap]
rs6544888	0.88[CEU][hapmap]
rs6544889	0.81[CEU][hapmap]
rs6544890	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6544898	0.82[YRI][hapmap]
rs6707241	0.85[CEU][hapmap];0.82[CHD][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs6735812	0.85[CEU][hapmap]
rs6740096	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs6743991	0.85[CEU][hapmap];0.89[MEX][hapmap];0.80[AMR][1000 genomes]
rs6756667	0.85[CEU][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs7557190	0.82[YRI][hapmap]
rs7567582	0.85[CEU][hapmap]
rs7568285	0.89[CEU][hapmap]
rs7583088	0.85[CEU][hapmap]
rs7583392	0.85[CEU][hapmap]
rs7594278	0.89[CEU][hapmap]
rs7594912	0.89[CEU][hapmap]
rs7598371	0.92[CEU][hapmap]
rs7606559	0.84[CEU][hapmap]
rs7607633	0.82[YRI][hapmap]
rs880671	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv916169	chr2:46310963-46622603	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	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
4	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

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46568000-46596600	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:46573200-46613000	Strong transcription	Hela-S3	cervix
3	chr2:46574600-46607200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:46574800-46613000	Weak transcription	HSMM	muscle
5	chr2:46580000-46594600	Weak transcription	Psoas Muscle	Psoas
6	chr2:46580600-46597200	Weak transcription	Fetal Heart	heart
7	chr2:46581200-46597000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:46585000-46593200	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:46585200-46594600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:46585400-46593200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:46585400-46594000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:46585600-46592600	Weak transcription	Brain Anterior Caudate	brain
13	chr2:46585600-46593200	Weak transcription	Brain Angular Gyrus	brain
14	chr2:46586600-46604000	Weak transcription	HSMMtube	muscle
15	chr2:46588600-46604800	Weak transcription	Stomach Mucosa	stomach
16	chr2:46588800-46596800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:46588800-46597200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:46588800-46598800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr2:46589000-46592600	Enhancers	Primary T cells from cord blood	blood
20	chr2:46589000-46594800	Genic enhancers	Liver	Liver
21	chr2:46589200-46593000	Genic enhancers	Adipose Nuclei	Adipose
22	chr2:46589200-46596200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:46589200-46597000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:46589400-46594600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:46589400-46596200	Weak transcription	Fetal Intestine Large	intestine
26	chr2:46589400-46596800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:46589600-46593600	Genic enhancers	A549	lung
28	chr2:46589600-46597000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:46589800-46593000	Weak transcription	Small Intestine	intestine
30	chr2:46589800-46594600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:46589800-46594600	Weak transcription	Spleen	Spleen
32	chr2:46589800-46594800	Weak transcription	Colonic Mucosa	Colon
33	chr2:46589800-46597000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:46589800-46616600	Weak transcription	Thymus	Thymus
35	chr2:46590000-46593200	Strong transcription	Placenta	Placenta
36	chr2:46590000-46594400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr2:46590000-46594800	Weak transcription	Right Ventricle	heart
38	chr2:46590000-46595400	Weak transcription	Fetal Thymus	thymus
39	chr2:46590200-46596400	Weak transcription	Esophagus	oesophagus
40	chr2:46590400-46593600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:46590400-46594400	Weak transcription	Fetal Intestine Small	intestine
42	chr2:46590400-46596400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:46590600-46592600	Weak transcription	NHEK	skin
44	chr2:46590600-46594400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr2:46591000-46593000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:46591000-46593000	Weak transcription	Fetal Stomach	stomach
47	chr2:46591000-46594600	Weak transcription	Aorta	Aorta
48	chr2:46591000-46594600	Weak transcription	Lung	lung
49	chr2:46591000-46594600	Weak transcription	Pancreas	Pancrea
50	chr2:46591000-46596200	Weak transcription	Ovary	ovary

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