Variant report

Variant	rs673496
Chromosome Location	chr10:5978795-5978796
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1052420	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs1323659	0.82[CEU][hapmap];1.00[MEX][hapmap]
rs1707228	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs2253422	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs2274030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs2669124	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2669127	0.82[CEU][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes]
rs2761269	0.96[ASN][1000 genomes]
rs2942348	0.96[ASN][1000 genomes]
rs2985042	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap]
rs2985043	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs2985044	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs584000	0.95[ASN][1000 genomes]
rs587620	0.96[ASN][1000 genomes]
rs587655	0.96[ASN][1000 genomes]
rs593026	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs596156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs599394	0.88[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs600706	0.95[ASN][1000 genomes]
rs608197	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs609269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs610335	0.96[ASN][1000 genomes]
rs615879	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs617165	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs622252	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs622488	0.96[ASN][1000 genomes]
rs625073	0.91[ASN][1000 genomes]
rs626040	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs627303	0.96[ASN][1000 genomes]
rs628175	0.95[ASN][1000 genomes]
rs628219	0.95[ASN][1000 genomes]
rs628234	0.95[ASN][1000 genomes]
rs628844	0.82[CEU][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs631538	0.85[ASN][1000 genomes]
rs632639	0.83[EUR][1000 genomes]
rs641034	0.82[EUR][1000 genomes]
rs644474	1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs646406	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs646490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs647391	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs661411	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs662701	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs664577	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs664842	0.96[ASN][1000 genomes]
rs665364	0.91[JPT][hapmap]
rs666831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs672219	0.85[ASN][1000 genomes]
rs672624	0.82[ASN][1000 genomes]
rs673678	0.96[ASN][1000 genomes]
rs675416	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs682555	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs684557	1.00[CHB][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs687191	0.96[ASN][1000 genomes]
rs7071536	0.84[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs7075778	0.82[CEU][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes]
rs7091817	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs792342	0.92[ASN][1000 genomes]
rs792347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs792349	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs811561	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs9329328	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9424023	0.96[ASN][1000 genomes]

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	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1041261	chr10:5962635-6052196	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1050983	chr10:5963921-6052196	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 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	chr10:5944000-5981600	Strong transcription	Fetal Intestine Small	intestine
2	chr10:5944600-5981200	Strong transcription	Fetal Thymus	thymus
3	chr10:5945800-5980800	Strong transcription	Thymus	Thymus
4	chr10:5947000-5980800	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr10:5947000-5981600	Strong transcription	Placenta	Placenta
6	chr10:5947200-5981000	Strong transcription	Fetal Intestine Large	intestine
7	chr10:5947400-5981200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr10:5947600-5981000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:5947600-5981000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr10:5947600-5981000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr10:5947600-5981000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr10:5947600-5981200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr10:5948400-5981000	Strong transcription	Duodenum Smooth Muscle	Duodenum
14	chr10:5948400-5981000	Strong transcription	Stomach Smooth Muscle	stomach
15	chr10:5948600-5981000	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr10:5948800-5981000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr10:5948800-5981000	Strong transcription	Duodenum Mucosa	Duodenum
18	chr10:5948800-5981600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr10:5950000-5980400	Strong transcription	Dnd41	blood
20	chr10:5950200-5981000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:5950600-5981000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr10:5950600-5981000	Strong transcription	Lung	lung
23	chr10:5950600-5981000	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr10:5950600-5981200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr10:5950800-5980600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr10:5950800-5980800	Strong transcription	GM12878-XiMat	blood
27	chr10:5952000-5985000	Weak transcription	Stomach Mucosa	stomach
28	chr10:5955000-5981400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr10:5960600-5981200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr10:5961000-5981200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr10:5965800-5981000	Strong transcription	A549	lung
32	chr10:5966200-5983600	Weak transcription	Right Atrium	heart
33	chr10:5969400-5982800	Strong transcription	Fetal Stomach	stomach
34	chr10:5969600-5987800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr10:5969600-6012000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr10:5969800-5980800	Strong transcription	HSMMtube	muscle
37	chr10:5969800-5981000	Strong transcription	Fetal Muscle Trunk	muscle
38	chr10:5969800-5981200	Strong transcription	Fetal Muscle Leg	muscle
39	chr10:5970000-5981600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr10:5970400-5981000	Strong transcription	Osteobl	bone
41	chr10:5971200-5981000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr10:5971400-6013200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr10:5971800-5983400	Weak transcription	Psoas Muscle	Psoas
44	chr10:5972200-5981000	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr10:5972400-5981000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr10:5972800-5986800	Weak transcription	Hela-S3	cervix
47	chr10:5973000-5980800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr10:5973400-5985600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr10:5974600-5980800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr10:5974800-5981000	Strong transcription	Primary monocytes fromperipheralblood	blood

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