Variant report

Variant	rs11255974
Chromosome Location	chr10:5968894-5968895
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10508298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10508299	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255698	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255774	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255780	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255971	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11256009	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12359234	1.00[CHB][hapmap]
rs12360409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12767690	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774228	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774886	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12777477	1.00[CHB][hapmap]
rs12781700	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12785055	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17319759	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976655	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985072	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2387092	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36049919	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3891620	0.95[YRI][hapmap]
rs56369297	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61832959	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6602330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7067928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082434	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090411	1.00[CHB][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7893735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7919913	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5933200-5977000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:5944000-5981600	Strong transcription	Fetal Intestine Small	intestine
3	chr10:5944600-5981200	Strong transcription	Fetal Thymus	thymus
4	chr10:5945800-5980800	Strong transcription	Thymus	Thymus
5	chr10:5947000-5980800	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr10:5947000-5981600	Strong transcription	Placenta	Placenta
7	chr10:5947200-5981000	Strong transcription	Fetal Intestine Large	intestine
8	chr10:5947400-5970800	Strong transcription	Liver	Liver
9	chr10:5947400-5974400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr10:5947400-5981200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr10:5947600-5975000	Strong transcription	Primary T cells from cord blood	blood
12	chr10:5947600-5981000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr10:5947600-5981000	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr10:5947600-5981000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr10:5947600-5981000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr10:5947600-5981200	Strong transcription	Primary B cells from peripheral blood	blood
17	chr10:5947800-5974000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr10:5947800-5974400	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr10:5947800-5974600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr10:5948000-5974600	Strong transcription	Fetal Lung	lung
21	chr10:5948000-5974800	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr10:5948000-5975000	Strong transcription	Primary B cells from cord blood	blood
23	chr10:5948000-5975800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr10:5948200-5974000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr10:5948200-5974800	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr10:5948400-5981000	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr10:5948400-5981000	Strong transcription	Stomach Smooth Muscle	stomach
28	chr10:5948600-5981000	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr10:5948800-5974200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr10:5948800-5981000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr10:5948800-5981000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr10:5948800-5981600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr10:5949400-5970200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr10:5949600-5975600	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr10:5949800-5973400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr10:5949800-5975000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr10:5950000-5976400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr10:5950000-5980400	Strong transcription	Dnd41	blood
39	chr10:5950200-5975800	Strong transcription	Brain Germinal Matrix	brain
40	chr10:5950200-5981000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr10:5950600-5973200	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr10:5950600-5973600	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr10:5950600-5974600	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr10:5950600-5975200	Strong transcription	Primary hematopoietic stem cells	blood
45	chr10:5950600-5981000	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr10:5950600-5981000	Strong transcription	Lung	lung
47	chr10:5950600-5981000	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr10:5950600-5981200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr10:5950800-5969000	Strong transcription	Brain Substantia Nigra	brain
50	chr10:5950800-5969200	Strong transcription	Brain Hippocampus Middle	brain

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