Variant report

Variant	rs3748945
Chromosome Location	chr2:55776793-55776794
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	chr2:55771544..55774381-chr2:55776715..55779906,3	K562	blood:
2	chr2:55745086..55746689-chr2:55776287..55778878,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1037508	0.95[ASN][1000 genomes]
rs10427222	0.82[ASW][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.90[YRI][hapmap]
rs1045910	0.87[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs10496044	0.83[YRI][hapmap]
rs10496049	0.86[YRI][hapmap]
rs11900763	0.81[CEU][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap]
rs12463766	0.93[ASN][1000 genomes]
rs12616502	0.96[YRI][hapmap]
rs12619756	0.87[ASN][1000 genomes]
rs12989898	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13016772	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs13028892	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.87[MKK][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs13382187	0.83[YRI][hapmap]
rs13383352	0.83[YRI][hapmap]
rs13403782	0.81[ASN][1000 genomes]
rs13407344	0.82[YRI][hapmap]
rs1563201	0.87[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs17047094	0.96[YRI][hapmap]
rs17047119	0.86[YRI][hapmap]
rs1975485	0.81[JPT][hapmap]
rs1975486	0.86[JPT][hapmap]
rs2168097	0.85[ASN][1000 genomes]
rs2586946	0.84[ASN][1000 genomes]
rs2586948	0.84[ASN][1000 genomes]
rs2586949	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs2586965	0.80[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2627758	0.85[ASN][1000 genomes]
rs2627763	0.83[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2627778	0.80[ASN][1000 genomes]
rs2627783	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3816489	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4233962	0.95[ASN][1000 genomes]
rs4671248	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[ASN][1000 genomes]
rs62165178	0.96[ASN][1000 genomes]
rs6545503	0.95[JPT][hapmap]
rs6545505	0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs6545508	0.86[YRI][hapmap]
rs6545510	0.96[YRI][hapmap]
rs6545513	0.83[YRI][hapmap]
rs6716100	0.86[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6717574	0.90[LWK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs6731927	0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs6739788	0.89[YRI][hapmap]
rs6745650	0.96[YRI][hapmap]
rs6760959	0.96[YRI][hapmap]
rs706549	0.87[CHD][hapmap]
rs706551	0.87[CHD][hapmap]
rs730884	0.95[ASN][1000 genomes]
rs736345	0.96[YRI][hapmap]
rs744514	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs7571482	0.84[ASN][1000 genomes]
rs7574409	0.80[AMR][1000 genomes]
rs7585484	0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7586124	0.87[LWK][hapmap]
rs7594497	0.83[YRI][hapmap]
rs7605486	0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7605504	0.86[ASN][1000 genomes]
rs782574	0.85[CHD][hapmap]
rs782583	0.87[CHD][hapmap]
rs782589	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs782591	0.84[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs782593	0.84[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs782598	0.84[ASN][1000 genomes]
rs782603	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs782612	0.85[ASN][1000 genomes]
rs782620	0.91[CHD][hapmap]
rs782636	0.87[CHD][hapmap]
rs782648	0.81[ASN][1000 genomes]
rs782651	0.81[ASN][1000 genomes]
rs9309267	0.96[YRI][hapmap]
rs9636439	0.82[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.90[YRI][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55747800-55784000	Weak transcription	Esophagus	oesophagus
2	chr2:55748000-55784000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:55748000-55788000	Weak transcription	Colonic Mucosa	Colon
4	chr2:55748000-55793800	Weak transcription	Psoas Muscle	Psoas
5	chr2:55748200-55777400	Weak transcription	NHLF	lung
6	chr2:55748200-55778800	Weak transcription	Fetal Heart	heart
7	chr2:55748200-55782400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:55752600-55788200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:55752600-55831400	Weak transcription	Stomach Mucosa	stomach
10	chr2:55753600-55786600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:55754000-55784000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:55754400-55783000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:55758200-55781200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:55758200-55783800	Weak transcription	Gastric	stomach
15	chr2:55758200-55784000	Weak transcription	Pancreas	Pancrea
16	chr2:55758600-55784000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr2:55760800-55788000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:55761000-55788200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:55761200-55777200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:55761400-55781600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:55762000-55783800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:55762200-55782600	Weak transcription	NHEK	skin
23	chr2:55762200-55784000	Weak transcription	Right Ventricle	heart
24	chr2:55762800-55781000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:55765000-55776800	Weak transcription	GM12878-XiMat	blood
26	chr2:55765200-55780200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:55766400-55783000	Weak transcription	Fetal Brain Male	brain
28	chr2:55767000-55784000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:55768600-55777200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:55768800-55778400	Strong transcription	Primary B cells from peripheral blood	blood
31	chr2:55769200-55777000	Strong transcription	HSMM	muscle
32	chr2:55769400-55777800	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr2:55769400-55778200	Strong transcription	Adipose Nuclei	Adipose
34	chr2:55769400-55778400	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:55769600-55777000	Strong transcription	Osteobl	bone
36	chr2:55769600-55777600	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:55769600-55778000	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr2:55769600-55778200	Strong transcription	Fetal Thymus	thymus
39	chr2:55769600-55778800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr2:55769600-55816000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:55769800-55777400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:55769800-55782600	Strong transcription	Fetal Intestine Large	intestine
43	chr2:55769800-55788200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:55770000-55778200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:55770000-55778600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr2:55770000-55787000	Strong transcription	Dnd41	blood
47	chr2:55770400-55818200	Weak transcription	Small Intestine	intestine
48	chr2:55770600-55821600	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr2:55770800-55778600	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr2:55770800-55815800	Strong transcription	Liver	Liver

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