Variant report

Variant	rs4880653
Chromosome Location	chr10:4022450-4022451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10795115	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10795116	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10795117	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10795118	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10904153	0.94[EUR][1000 genomes]
rs10904163	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10904164	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10904165	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11252218	0.95[EUR][1000 genomes]
rs11252222	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11252232	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11252238	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11252240	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11252241	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11252242	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11252243	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2031578	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2148188	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2148189	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34133718	0.90[EUR][1000 genomes]
rs4242767	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4880652	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4881258	0.81[CHD][hapmap]
rs7072577	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7079191	0.94[EUR][1000 genomes]
rs7098821	0.81[CEU][hapmap];0.80[GIH][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs7920244	0.94[EUR][1000 genomes]
rs7922194	0.96[EUR][1000 genomes]

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	nsv1043680	chr10:3551191-4038002	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv1051297	chr10:3908706-4277678	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
3	nsv894784	chr10:3985194-4051081	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv5609	chr10:4002849-4040114	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:4017400-4025200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr10:4017400-4025400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr10:4017800-4025200	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr10:4018000-4024400	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr10:4018200-4022800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr10:4018200-4024400	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr10:4018200-4025200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr10:4020200-4025200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr10:4020200-4032600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr10:4020400-4022800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr10:4020600-4023600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr10:4020800-4022800	Enhancers	Primary T cells fromperipheralblood	blood
13	chr10:4020800-4024200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr10:4020800-4024400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr10:4021000-4022800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr10:4021000-4023600	Enhancers	Dnd41	blood
17	chr10:4021200-4023600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr10:4021200-4024400	Enhancers	Primary T cells from cord blood	blood
19	chr10:4021200-4027200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr10:4021400-4022600	Enhancers	Colonic Mucosa	Colon
21	chr10:4021400-4022800	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr10:4021800-4023000	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr10:4021800-4024200	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr10:4022000-4022600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr10:4022000-4022600	Enhancers	Fetal Thymus	thymus
26	chr10:4022000-4022600	Enhancers	Spleen	Spleen
27	chr10:4022000-4023800	Enhancers	Primary hematopoietic stem cells	blood
28	chr10:4022000-4023800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr10:4022000-4024600	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr10:4022200-4022600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr10:4022200-4022600	Enhancers	Esophagus	oesophagus
32	chr10:4022200-4022600	Enhancers	Fetal Intestine Small	intestine
33	chr10:4022200-4036400	Weak transcription	Right Atrium	heart
34	chr10:4022400-4023400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr10:4022400-4023800	Enhancers	GM12878-XiMat	blood
36	chr10:4022400-4023800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr10:4022400-4024000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr10:4022400-4024000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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