Variant report

Variant	rs6836390
Chromosome Location	chr4:102119063-102119064
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr4:102118455-102119117	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:102112038..102115219-chr4:102118263..102121528,3	MCF-7	breast:
2	chr4:102119014..102119905-chr4:102132461..102133442,2	MCF-7	breast:
3	chr4:102115439..102118195-chr4:102118309..102119810,2	MCF-7	breast:

Variant related genes	Relation type
PPP3CA	TF binding region
ENSG00000138814	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11935869	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3730251	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57300146	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73833259	0.81[AFR][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	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:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102104400-102119400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr4:102104400-102119600	Weak transcription	Primary T cells from cord blood	blood
3	chr4:102104400-102119600	Weak transcription	Ovary	ovary
4	chr4:102105400-102126200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr4:102106200-102121600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:102107600-102126600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr4:102109200-102126200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr4:102109600-102119400	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr4:102109800-102122600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr4:102111200-102122400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr4:102111800-102119600	Weak transcription	Fetal Brain Female	brain
12	chr4:102113200-102119800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:102113200-102119800	Weak transcription	Fetal Brain Male	brain
14	chr4:102113200-102121000	Weak transcription	HSMM	muscle
15	chr4:102113200-102122400	Weak transcription	Aorta	Aorta
16	chr4:102113200-102124400	Weak transcription	Pancreas	Pancrea
17	chr4:102113400-102120400	Weak transcription	Fetal Heart	heart
18	chr4:102113400-102120800	Weak transcription	NH-A	brain
19	chr4:102113600-102119400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr4:102113600-102119600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr4:102113600-102119600	Weak transcription	Brain Angular Gyrus	brain
22	chr4:102113600-102120600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr4:102113600-102120800	Weak transcription	Right Ventricle	heart
24	chr4:102113600-102121400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:102113600-102122800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:102113800-102119600	Weak transcription	Brain Hippocampus Middle	brain
27	chr4:102113800-102119600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr4:102113800-102119600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr4:102113800-102119600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr4:102113800-102119800	Weak transcription	Fetal Kidney	kidney
31	chr4:102113800-102120400	Weak transcription	Brain Substantia Nigra	brain
32	chr4:102113800-102120600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:102113800-102120800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:102113800-102121000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr4:102113800-102121000	Weak transcription	HMEC	breast
36	chr4:102113800-102122800	Weak transcription	Right Atrium	heart
37	chr4:102113800-102126200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:102113800-102127200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr4:102113800-102131800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr4:102114000-102119800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr4:102114000-102120000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr4:102114000-102120600	Weak transcription	NHDF-Ad	bronchial
43	chr4:102114000-102121200	Weak transcription	Adipose Nuclei	Adipose
44	chr4:102114200-102119200	Weak transcription	Brain Anterior Caudate	brain
45	chr4:102114200-102119400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr4:102114800-102121200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr4:102115400-102120800	Weak transcription	Osteobl	bone
48	chr4:102117000-102120800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:102117000-102121600	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr4:102117200-102119400	Weak transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links