Variant report

Variant	rs6762788
Chromosome Location	chr3:52792311-52792312
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10510759	1.00[CEU][hapmap]
rs11510435	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12107484	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17052357	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17052404	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1963813	0.91[AFR][1000 genomes]
rs34173244	1.00[EUR][1000 genomes]
rs4532127	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56134416	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56156188	1.00[EUR][1000 genomes]
rs56276589	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56665533	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57008939	1.00[EUR][1000 genomes]
rs57298447	1.00[EUR][1000 genomes]
rs57757646	1.00[EUR][1000 genomes]
rs57789542	1.00[EUR][1000 genomes]
rs57869735	1.00[EUR][1000 genomes]
rs57946083	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58409398	1.00[EUR][1000 genomes]
rs58528592	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58564212	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59638016	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59869286	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60040519	1.00[EUR][1000 genomes]
rs60058353	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60256157	1.00[EUR][1000 genomes]
rs60311166	1.00[EUR][1000 genomes]
rs60770874	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60830326	1.00[EUR][1000 genomes]
rs61220667	1.00[EUR][1000 genomes]
rs61538294	1.00[EUR][1000 genomes]
rs6445536	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6769720	1.00[EUR][1000 genomes]
rs6780005	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6780397	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6803492	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs72950424	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72950432	1.00[EUR][1000 genomes]
rs72950437	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960212	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960237	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960240	1.00[EUR][1000 genomes]
rs72960260	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960274	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960281	1.00[EUR][1000 genomes]
rs72960285	1.00[EUR][1000 genomes]
rs72965177	1.00[EUR][1000 genomes]
rs72965181	1.00[EUR][1000 genomes]
rs73839126	1.00[EUR][1000 genomes]
rs73839129	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7645785	1.00[EUR][1000 genomes]
rs764636	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7647992	1.00[EUR][1000 genomes]
rs934839	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv508219	chr3:52741193-52803899	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
4	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52741600-52804000	Weak transcription	Psoas Muscle	Psoas
2	chr3:52761600-52802400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:52763800-52802600	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:52764000-52800200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:52764000-52802800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:52764400-52802600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:52765200-52793400	Strong transcription	Fetal Intestine Large	intestine
8	chr3:52765400-52800400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:52766400-52802600	Strong transcription	Fetal Thymus	thymus
10	chr3:52767600-52802600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:52767600-52803400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:52767800-52793000	Weak transcription	Small Intestine	intestine
13	chr3:52767800-52800600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:52768000-52803600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:52768400-52797200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:52768800-52803000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:52770200-52797200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:52771200-52800800	Strong transcription	Fetal Lung	lung
19	chr3:52772600-52794800	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:52774000-52803400	Weak transcription	K562	blood
21	chr3:52775200-52800600	Strong transcription	Stomach Smooth Muscle	stomach
22	chr3:52775200-52802600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:52775800-52802800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:52775800-52802800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:52776000-52794200	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr3:52778400-52802400	Strong transcription	Liver	Liver
27	chr3:52779400-52793800	Weak transcription	NHLF	lung
28	chr3:52781000-52792800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:52781000-52796000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:52781000-52799000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:52782600-52801000	Strong transcription	Dnd41	blood
32	chr3:52783200-52803800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr3:52784800-52804000	Weak transcription	Aorta	Aorta
34	chr3:52785400-52797800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:52785800-52793400	Strong transcription	Rectal Smooth Muscle	rectum
36	chr3:52786000-52802000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr3:52786200-52793400	Weak transcription	Fetal Heart	heart
38	chr3:52786200-52798800	Weak transcription	HMEC	breast
39	chr3:52786200-52803600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr3:52786400-52792800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:52786400-52803600	Weak transcription	Stomach Mucosa	stomach
42	chr3:52786400-52803800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:52786600-52792600	Weak transcription	Hela-S3	cervix
44	chr3:52786600-52793400	Weak transcription	GM12878-XiMat	blood
45	chr3:52786600-52795800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr3:52786600-52802600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:52786800-52802600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:52786800-52802600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:52787400-52796000	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr3:52787400-52796000	Strong transcription	Monocytes-CD14+_RO01746	blood

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