Variant report

Variant	rs16873317
Chromosome Location	chr5:75627770-75627771
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IQGAP2-1	chr5:75627662-75629781	ENSG00000266045.1

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11954110	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11954779	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16873320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17566966	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55712299	0.94[AFR][1000 genomes]
rs60514411	0.88[AFR][1000 genomes]
rs60691295	0.94[AFR][1000 genomes]
rs73764325	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73764326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73764327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73764328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73764330	0.94[AFR][1000 genomes]
rs73764331	0.94[AFR][1000 genomes]
rs73764332	0.94[AFR][1000 genomes]
rs73764346	0.94[AFR][1000 genomes]
rs73764347	0.94[AFR][1000 genomes]
rs73764349	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv870415	chr5:75526088-75738412	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1032033	chr5:75609686-75646482	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1023310	chr5:75609686-75651786	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv3353515	chr5:75609996-75632294	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv3425598	chr5:75610980-75647048	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv2757120	chr5:75611597-75642974	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv2759352	chr5:75611597-75642974	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1028669	chr5:75611597-75643598	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1020853	chr5:75611597-75651786	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv598678	chr5:75614737-75628413	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75620400-75629400	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr5:75620600-75629600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr5:75620600-75630400	Enhancers	Primary hematopoietic stem cells	blood
4	chr5:75621400-75627800	Weak transcription	Pancreas	Pancrea
5	chr5:75622000-75629800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr5:75622200-75629000	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr5:75622600-75633600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:75622800-75634000	Weak transcription	Esophagus	oesophagus
9	chr5:75623200-75628000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr5:75623200-75628600	Weak transcription	Fetal Lung	lung
11	chr5:75623200-75628800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:75624000-75629600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:75624600-75629600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr5:75624800-75628800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr5:75625800-75628400	Enhancers	Primary T cells fromperipheralblood	blood
16	chr5:75626000-75628200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr5:75626000-75629000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:75626200-75628200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr5:75626800-75627800	Enhancers	Adipose Nuclei	Adipose
20	chr5:75626800-75628000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr5:75626800-75628800	Enhancers	Fetal Thymus	thymus
22	chr5:75626800-75631000	Enhancers	Fetal Stomach	stomach
23	chr5:75627000-75627800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr5:75627000-75627800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr5:75627000-75627800	Enhancers	Thymus	Thymus
26	chr5:75627000-75628000	Enhancers	H9 Cell Line	embryonic stem cell
27	chr5:75627000-75628000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:75627000-75628000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr5:75627000-75628000	Enhancers	Placenta	Placenta
30	chr5:75627000-75628200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr5:75627000-75628200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:75627000-75628200	Enhancers	Fetal Muscle Leg	muscle
33	chr5:75627000-75628600	Enhancers	Fetal Intestine Small	intestine
34	chr5:75627000-75628600	Enhancers	Stomach Mucosa	stomach
35	chr5:75627000-75628800	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr5:75627000-75629000	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr5:75627000-75629000	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr5:75627000-75629000	Flanking Active TSS	HepG2	liver
39	chr5:75627000-75629600	Enhancers	K562	blood
40	chr5:75627200-75627800	Enhancers	Dnd41	blood
41	chr5:75627200-75628200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:75627200-75628200	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr5:75627200-75628400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr5:75627200-75628600	Enhancers	H1 Cell Line	embryonic stem cell
45	chr5:75627200-75628600	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr5:75627200-75628600	Enhancers	Liver	Liver
47	chr5:75627200-75628800	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr5:75627400-75628000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr5:75627400-75628200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr5:75627400-75628200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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