Variant report

Variant	rs3804368
Chromosome Location	chr4:102127559-102127560
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10005338	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10018021	0.84[EUR][1000 genomes]
rs10025780	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10030389	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs10050301	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10516471	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13103902	0.83[EUR][1000 genomes]
rs13111186	0.83[EUR][1000 genomes]
rs13112866	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13118966	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13125501	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13128841	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs13135924	0.83[EUR][1000 genomes]
rs13142024	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2048072	0.96[CEU][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2135611	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2174680	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3804361	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3811063	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827770	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4590038	0.83[EUR][1000 genomes]
rs4698912	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs4698913	0.83[EUR][1000 genomes]
rs4699106	0.83[EUR][1000 genomes]
rs4699116	0.95[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699127	0.95[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7677550	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs950177	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9884638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9995338	0.84[EUR][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	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:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102113800-102131800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr4:102118000-102132600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:102120000-102131400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:102121800-102128600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr4:102121800-102131200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr4:102121800-102132600	Weak transcription	Colon Smooth Muscle	Colon
7	chr4:102122000-102132400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr4:102123000-102129400	Weak transcription	Right Ventricle	heart
9	chr4:102123200-102131400	Weak transcription	Aorta	Aorta
10	chr4:102123200-102131600	Weak transcription	Small Intestine	intestine
11	chr4:102123200-102132200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:102123200-102132200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:102123200-102132200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:102123200-102132400	Weak transcription	NHEK	skin
15	chr4:102123200-102133400	Weak transcription	Psoas Muscle	Psoas
16	chr4:102123200-102133400	Weak transcription	Right Atrium	heart
17	chr4:102123400-102132800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr4:102124200-102132800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr4:102125200-102129600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr4:102125800-102128200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:102125800-102129600	Enhancers	Dnd41	blood
22	chr4:102126000-102129000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:102126200-102128000	Enhancers	A549	lung
24	chr4:102126200-102128200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr4:102126200-102128200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:102126200-102128400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr4:102126200-102128600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr4:102126200-102129000	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr4:102126200-102129000	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr4:102126400-102129000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:102126600-102127800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:102126600-102127800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:102126600-102127800	Enhancers	Muscle Satellite Cultured Cells	--
34	chr4:102126600-102127800	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr4:102126600-102127800	Enhancers	Osteobl	bone
36	chr4:102126600-102128000	Enhancers	Brain Anterior Caudate	brain
37	chr4:102126600-102128200	Enhancers	Primary T cells fromperipheralblood	blood
38	chr4:102126600-102128200	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr4:102126600-102128200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr4:102126600-102128200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr4:102126600-102128400	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr4:102126800-102128200	Enhancers	Primary hematopoietic stem cells	blood
43	chr4:102127000-102127600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:102127000-102128000	Enhancers	Brain Hippocampus Middle	brain
45	chr4:102127000-102128200	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr4:102127000-102128200	Enhancers	Primary B cells from peripheral blood	blood
47	chr4:102127200-102128000	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr4:102127200-102128600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr4:102127200-102132200	Weak transcription	HSMM	muscle
50	chr4:102127400-102127600	Flanking Active TSS	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links