Variant report

Variant	rs1406311
Chromosome Location	chr4:99495460-99495461
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:99494665..99495526-chr4:99539142..99539720,2	MCF-7	breast:
2	chr4:99494205..99497159-chr4:99499484..99501729,2	MCF-7	breast:
3	chr4:99494775..99495594-chr4:99505088..99505683,2	MCF-7	breast:
4	chr4:99435319..99436156-chr4:99495025..99495627,2	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11944636	1.00[CEU][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1547382	0.85[CEU][hapmap]
rs17027776	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17027777	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17027779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17027799	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv2760882	chr4:99460485-99521345	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99466800-99501600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr4:99479000-99506400	Weak transcription	Aorta	Aorta
3	chr4:99483200-99495800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:99483400-99498800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:99485000-99501400	Weak transcription	HUVEC	blood vessel
6	chr4:99487200-99500000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr4:99487800-99498600	Weak transcription	NHLF	lung
8	chr4:99488000-99499000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr4:99488000-99499200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:99488200-99495800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:99488200-99500200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr4:99489000-99498800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr4:99490200-99499000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr4:99490400-99499200	Weak transcription	Brain Germinal Matrix	brain
15	chr4:99490600-99498600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:99490600-99498800	Weak transcription	Stomach Mucosa	stomach
17	chr4:99490600-99501400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr4:99490800-99499600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:99490800-99499800	Weak transcription	Right Atrium	heart
20	chr4:99490800-99506600	Weak transcription	Esophagus	oesophagus
21	chr4:99490800-99509000	Weak transcription	HSMM	muscle
22	chr4:99491000-99503400	Weak transcription	Thymus	Thymus
23	chr4:99491600-99495600	Weak transcription	Ovary	ovary
24	chr4:99492000-99495800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr4:99492000-99496200	Weak transcription	NHDF-Ad	bronchial
26	chr4:99492000-99498600	Weak transcription	Fetal Muscle Leg	muscle
27	chr4:99492000-99499200	Weak transcription	Osteobl	bone
28	chr4:99492400-99498800	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr4:99492600-99495600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:99492600-99497200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:99492600-99498600	Weak transcription	Brain Anterior Caudate	brain
32	chr4:99492600-99499800	Weak transcription	Spleen	Spleen
33	chr4:99492600-99500200	Weak transcription	Fetal Brain Female	brain
34	chr4:99492600-99501800	Weak transcription	Primary B cells from cord blood	blood
35	chr4:99492800-99497800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr4:99493200-99501400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr4:99493600-99495600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr4:99493600-99498800	Weak transcription	Brain Hippocampus Middle	brain
39	chr4:99493600-99500400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr4:99493600-99501400	Weak transcription	Fetal Thymus	thymus
41	chr4:99493800-99498800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr4:99494000-99499200	Weak transcription	Fetal Lung	lung
43	chr4:99494200-99498600	Weak transcription	Brain Angular Gyrus	brain
44	chr4:99494200-99498600	Weak transcription	Brain Substantia Nigra	brain
45	chr4:99494400-99495600	Weak transcription	Fetal Stomach	stomach
46	chr4:99494400-99495800	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr4:99494800-99495600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:99494800-99496000	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr4:99495000-99495600	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr4:99495000-99495800	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links