Variant report

Variant	rs40984
Chromosome Location	chr5:16931107-16931108
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:16930256..16932203-chr5:16934873..16936431,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145555	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs13354237	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2016972	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2016983	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2016997	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2170642	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2217341	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2434960	0.87[ASN][1000 genomes]
rs2434962	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2434965	0.80[EUR][1000 genomes]
rs2449479	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2454879	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs249137	0.84[ASN][1000 genomes]
rs249138	0.84[ASN][1000 genomes]
rs2562351	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2562361	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2562362	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2562363	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2562364	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2562365	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2562366	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2562367	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2625177	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2625178	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2625179	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2625180	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2625181	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2625182	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2625183	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2625184	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2625185	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2625186	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2625187	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2625188	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2625191	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2650457	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2650458	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2650459	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2650461	0.81[AMR][1000 genomes]
rs2650462	0.80[AMR][1000 genomes]
rs31452	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs31453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs31464	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs922881	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[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	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv2762500	chr5:16815489-16952565	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	esv3485757	chr5:16856475-16966851	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	esv3485758	chr5:16856475-16966851	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16904400-16933200	Weak transcription	Fetal Stomach	stomach
2	chr5:16914000-16931600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:16914000-16933200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:16914600-16934400	Weak transcription	Psoas Muscle	Psoas
5	chr5:16919200-16931600	Weak transcription	HMEC	breast
6	chr5:16922000-16931400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:16922000-16931600	Weak transcription	Osteobl	bone
8	chr5:16923200-16932400	Weak transcription	Gastric	stomach
9	chr5:16924600-16931600	Weak transcription	Fetal Intestine Small	intestine
10	chr5:16926200-16933200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:16928200-16931600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:16929600-16933400	Enhancers	Stomach Mucosa	stomach
13	chr5:16929600-16933600	Enhancers	Pancreas	Pancrea
14	chr5:16929800-16933200	Enhancers	Fetal Lung	lung
15	chr5:16929800-16933800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:16930000-16931200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr5:16930000-16931200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr5:16930000-16931600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:16930000-16931600	Enhancers	HUVEC	blood vessel
20	chr5:16930200-16931600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr5:16930200-16931800	Enhancers	H1 Cell Line	embryonic stem cell
22	chr5:16930200-16932600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:16930200-16932800	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr5:16930200-16932800	Enhancers	NHDF-Ad	bronchial
25	chr5:16930200-16933400	Enhancers	Ovary	ovary
26	chr5:16930200-16934000	Enhancers	Fetal Intestine Large	intestine
27	chr5:16930200-16934000	Enhancers	Fetal Muscle Leg	muscle
28	chr5:16930400-16931400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:16930400-16931600	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr5:16930400-16931600	Enhancers	Muscle Satellite Cultured Cells	--
31	chr5:16930400-16931800	Enhancers	HSMMtube	muscle
32	chr5:16930400-16931800	Genic enhancers	NHEK	skin
33	chr5:16930400-16933000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:16930400-16933000	Enhancers	HSMM	muscle
35	chr5:16930400-16933200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:16930400-16933200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:16930600-16931400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr5:16930600-16931800	Enhancers	H9 Cell Line	embryonic stem cell
39	chr5:16930600-16931800	Enhancers	Spleen	Spleen
40	chr5:16930600-16932000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr5:16930600-16932000	Enhancers	Small Intestine	intestine
42	chr5:16930600-16932200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr5:16930600-16932400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr5:16930600-16932400	Enhancers	NH-A	brain
45	chr5:16930600-16932400	Enhancers	NHLF	lung
46	chr5:16930600-16932600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr5:16930600-16932600	Enhancers	Duodenum Mucosa	Duodenum
48	chr5:16930800-16931200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr5:16930800-16931400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:16930800-16931800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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