Variant report

Variant	rs1393098
Chromosome Location	chr5:75902533-75902534
allele	C/T
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	chr5:75902320-75903018	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:75901625..75904371-chr5:75985828..75988323,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-F2RL2-1	chr5:75902433-75903909	ENSG00000249713.1

Variant related genes	Relation type
IQGAP2	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11948140	1.00[CEU][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951829	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11952193	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11952962	1.00[CEU][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1501689	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16873476	0.85[CEU][hapmap];0.85[CHD][hapmap];0.91[ASN][1000 genomes]
rs16873483	1.00[CEU][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16873519	0.93[ASW][hapmap];0.93[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2005247	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736395	0.93[ASW][hapmap];0.85[CEU][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3913473	0.91[ASN][1000 genomes]
rs3913474	0.91[ASN][1000 genomes]
rs3913475	0.92[CEU][hapmap];0.91[ASN][1000 genomes]
rs4704328	0.91[CEU][hapmap]
rs4704335	0.91[ASN][1000 genomes]
rs4704337	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4704341	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704342	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704343	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704344	1.00[CEU][hapmap];0.89[GIH][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62361989	0.91[ASN][1000 genomes]
rs62361990	0.83[ASN][1000 genomes]
rs62361991	0.91[ASN][1000 genomes]
rs62361992	0.83[ASN][1000 genomes]
rs62361997	0.91[ASN][1000 genomes]
rs62362011	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62362012	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62362013	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62362014	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62362016	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62362017	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62362019	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362020	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362022	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362035	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362036	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362037	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362038	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362039	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362042	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62362043	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72777520	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72777522	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022032	chr5:75785106-75914003	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS 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	3 gene(s)	inside rSNPs	diseases
2	nsv598679	chr5:75823965-75914729	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS 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	2 gene(s)	inside rSNPs	diseases
3	nsv1023953	chr5:75831037-75913784	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026257	chr5:75831037-75914003	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1016823	chr5:75831037-75915905	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv598680	chr5:75839165-75914729	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS 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	2 gene(s)	inside rSNPs	diseases
8	nsv598681	chr5:75863987-75902533	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1393098	IQGAP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75846800-75902600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr5:75873600-75903600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:75877000-75902800	Weak transcription	Adipose Nuclei	Adipose
4	chr5:75877400-75902800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr5:75879000-75913600	Weak transcription	Colonic Mucosa	Colon
6	chr5:75879000-75917600	Weak transcription	Fetal Thymus	thymus
7	chr5:75879000-75934000	Weak transcription	Small Intestine	intestine
8	chr5:75879200-75907400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:75879200-75919000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:75879400-75903400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:75880200-75933400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr5:75882600-75969400	Weak transcription	Stomach Mucosa	stomach
13	chr5:75883400-75904200	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr5:75884000-75903000	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr5:75884000-75914600	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr5:75884400-75919200	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr5:75884400-75919400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr5:75885400-75905000	Strong transcription	Primary hematopoietic stem cells	blood
19	chr5:75886200-75902800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr5:75889400-75903000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr5:75889400-75903000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr5:75891000-75911800	Weak transcription	Thymus	Thymus
23	chr5:75891200-75909200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:75891200-75911800	Strong transcription	Liver	Liver
25	chr5:75892000-75904000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr5:75892000-75910400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr5:75893400-75903400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr5:75893400-75903400	Weak transcription	Spleen	Spleen
29	chr5:75893600-75902600	Weak transcription	Gastric	stomach
30	chr5:75893600-75903200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr5:75895200-75912800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr5:75896800-75913800	Weak transcription	Pancreas	Pancrea
33	chr5:75897600-75902600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:75898000-75908800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr5:75898800-75902600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:75899200-75903400	Weak transcription	Esophagus	oesophagus
37	chr5:75899200-75904400	Weak transcription	K562	blood
38	chr5:75899400-75902600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:75899600-75902600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr5:75899600-75903000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr5:75899600-75907200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr5:75899800-75903200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr5:75900200-75902600	Enhancers	NHDF-Ad	bronchial
44	chr5:75900200-75903000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:75900400-75903000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr5:75900400-75903200	Enhancers	Osteobl	bone
47	chr5:75900400-75905200	Strong transcription	Duodenum Mucosa	Duodenum
48	chr5:75900800-75902600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr5:75900800-75907400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr5:75901000-75902600	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links