Variant report

Variant	rs248342
Chromosome Location	chr5:95199932-95199933
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:95199646..95202540-chr5:95204108..95206460,2	MCF-7	breast:
2	chr5:95199907..95202755-chr5:95294565..95297525,3	MCF-7	breast:
3	chr5:95193159..95197035-chr5:95199083..95201765,3	K562	blood:
4	chr5:95177864..95180977-chr5:95197821..95200225,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118985	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11135439	1.00[CHB][hapmap]
rs154447	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154448	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs154449	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17463444	1.00[CHB][hapmap]
rs17464446	1.00[CHB][hapmap]
rs248338	0.95[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248341	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs257683	1.00[CHB][hapmap]
rs6556889	1.00[CHB][hapmap]
rs6891719	1.00[CHB][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	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1019566	chr5:95180352-95300677	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95179000-95206000	Weak transcription	Spleen	Spleen
2	chr5:95192000-95201400	Enhancers	Placenta	Placenta
3	chr5:95194000-95200800	Weak transcription	Gastric	stomach
4	chr5:95194200-95203000	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr5:95195000-95200200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:95195000-95200600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr5:95195000-95206400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:95195000-95208400	Weak transcription	Ovary	ovary
9	chr5:95195200-95200600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr5:95195200-95217400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr5:95195400-95201600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:95195600-95206200	Weak transcription	Brain Anterior Caudate	brain
13	chr5:95195800-95201000	Weak transcription	Brain Substantia Nigra	brain
14	chr5:95195800-95201200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr5:95195800-95201200	Enhancers	NHLF	lung
16	chr5:95196800-95202000	Enhancers	Fetal Intestine Small	intestine
17	chr5:95196800-95203000	Enhancers	Fetal Intestine Large	intestine
18	chr5:95197000-95200000	Enhancers	Small Intestine	intestine
19	chr5:95197000-95201200	Enhancers	Left Ventricle	heart
20	chr5:95197000-95201800	Enhancers	Stomach Mucosa	stomach
21	chr5:95197200-95201200	Enhancers	NHDF-Ad	bronchial
22	chr5:95197200-95203200	Enhancers	Muscle Satellite Cultured Cells	--
23	chr5:95197400-95200000	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr5:95197400-95200600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr5:95197400-95201200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:95197600-95200000	Enhancers	HSMM	muscle
27	chr5:95197800-95200400	Enhancers	Adipose Nuclei	Adipose
28	chr5:95197800-95201200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:95197800-95204800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr5:95198200-95202600	Weak transcription	HMEC	breast
31	chr5:95198400-95200000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr5:95198600-95206200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr5:95198800-95200000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:95198800-95200000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:95198800-95200000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:95198800-95200000	Enhancers	Stomach Smooth Muscle	stomach
37	chr5:95198800-95200400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:95198800-95200600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr5:95199000-95200000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:95199000-95200000	Weak transcription	Colonic Mucosa	Colon
41	chr5:95199000-95200200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr5:95199000-95204200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr5:95199000-95204200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr5:95199200-95200200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:95199200-95200200	Weak transcription	Brain Hippocampus Middle	brain
46	chr5:95199200-95200400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr5:95199200-95200600	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr5:95199200-95200600	Weak transcription	Right Atrium	heart
49	chr5:95199200-95202000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:95199200-95202600	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links