Variant report

Variant	rs3804366
Chromosome Location	chr4:102125929-102125930
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1157038	0.89[CEU][hapmap]
rs1354785	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1395475	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1395476	0.89[CEU][hapmap]
rs1506799	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1506800	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1506802	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1506803	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1506804	0.88[CEU][hapmap]
rs1543856	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2135609	0.89[CEU][hapmap]
rs2135610	0.89[CEU][hapmap]
rs2135612	0.88[CEU][hapmap]
rs2659503	0.89[CEU][hapmap]
rs2659504	0.88[CEU][hapmap]
rs2659505	0.85[CEU][hapmap]
rs2659506	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2659508	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2659509	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659511	0.90[CEU][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659512	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659513	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659522	0.88[CEU][hapmap]
rs2659525	0.89[CEU][hapmap]
rs2659530	0.89[CEU][hapmap]
rs2659531	0.89[CEU][hapmap]
rs2659532	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659533	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2659534	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2659537	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659538	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659539	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659540	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659541	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659542	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850981	0.89[CEU][hapmap]
rs2850982	0.88[CEU][hapmap]
rs2850985	0.90[CEU][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2850987	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2850989	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850990	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2850991	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850994	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2850995	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2850998	0.89[CEU][hapmap]
rs2851003	0.89[CEU][hapmap]
rs970071	0.89[CEU][hapmap]

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	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102105400-102126200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr4:102107600-102126600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr4:102109200-102126200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr4:102113800-102126200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr4:102113800-102127200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:102113800-102131800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:102117200-102126200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr4:102118000-102132600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:102118200-102126800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr4:102118800-102126200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr4:102119600-102126200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr4:102120000-102131400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:102120600-102126600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr4:102121000-102126600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr4:102121600-102127000	Weak transcription	Brain Hippocampus Middle	brain
16	chr4:102121800-102126600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr4:102121800-102128600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:102121800-102131200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr4:102121800-102132600	Weak transcription	Colon Smooth Muscle	Colon
20	chr4:102122000-102127000	Weak transcription	HSMM	muscle
21	chr4:102122000-102132400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:102122600-102127000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:102122800-102126200	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr4:102122800-102126600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr4:102122800-102126800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr4:102123000-102126600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:102123000-102126600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr4:102123000-102126600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:102123000-102126600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr4:102123000-102126800	Weak transcription	NH-A	brain
31	chr4:102123000-102127000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr4:102123000-102127000	Weak transcription	NHDF-Ad	bronchial
33	chr4:102123000-102129400	Weak transcription	Right Ventricle	heart
34	chr4:102123200-102126600	Weak transcription	Osteobl	bone
35	chr4:102123200-102126800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:102123200-102127000	Weak transcription	Primary B cells from peripheral blood	blood
37	chr4:102123200-102127000	Weak transcription	HMEC	breast
38	chr4:102123200-102131400	Weak transcription	Aorta	Aorta
39	chr4:102123200-102131600	Weak transcription	Small Intestine	intestine
40	chr4:102123200-102132200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:102123200-102132200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:102123200-102132200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr4:102123200-102132400	Weak transcription	NHEK	skin
44	chr4:102123200-102133400	Weak transcription	Psoas Muscle	Psoas
45	chr4:102123200-102133400	Weak transcription	Right Atrium	heart
46	chr4:102123400-102132800	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr4:102124200-102126600	Weak transcription	Brain Anterior Caudate	brain
48	chr4:102124200-102132800	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr4:102124400-102126200	Weak transcription	A549	lung
50	chr4:102125200-102129600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links