Variant report

Variant	rs62362035
Chromosome Location	chr5:75903311-75903312
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	chr5:75901625..75904371-chr5:75985828..75988323,2	MCF-7	breast:

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

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11948140	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951829	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11952193	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11952962	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393098	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1501689	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16873476	0.91[ASN][1000 genomes]
rs16873483	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16873519	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	0.83[AFR][1000 genomes];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	0.91[ASN][1000 genomes]
rs4704335	0.91[ASN][1000 genomes]
rs4704337	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4704341	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704342	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704343	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704344	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	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362020	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362022	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362039	1.00[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	0.97[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	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62362035	IQGAP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75873600-75903600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:75879000-75913600	Weak transcription	Colonic Mucosa	Colon
3	chr5:75879000-75917600	Weak transcription	Fetal Thymus	thymus
4	chr5:75879000-75934000	Weak transcription	Small Intestine	intestine
5	chr5:75879200-75907400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:75879200-75919000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:75879400-75903400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:75880200-75933400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr5:75882600-75969400	Weak transcription	Stomach Mucosa	stomach
10	chr5:75883400-75904200	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr5:75884000-75914600	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr5:75884400-75919200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr5:75884400-75919400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr5:75885400-75905000	Strong transcription	Primary hematopoietic stem cells	blood
15	chr5:75891000-75911800	Weak transcription	Thymus	Thymus
16	chr5:75891200-75909200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:75891200-75911800	Strong transcription	Liver	Liver
18	chr5:75892000-75904000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr5:75892000-75910400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr5:75893400-75903400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr5:75893400-75903400	Weak transcription	Spleen	Spleen
22	chr5:75895200-75912800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr5:75896800-75913800	Weak transcription	Pancreas	Pancrea
24	chr5:75898000-75908800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:75899200-75903400	Weak transcription	Esophagus	oesophagus
26	chr5:75899200-75904400	Weak transcription	K562	blood
27	chr5:75899600-75907200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr5:75900400-75905200	Strong transcription	Duodenum Mucosa	Duodenum
29	chr5:75900800-75907400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr5:75901000-75906800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr5:75901200-75904800	Weak transcription	A549	lung
32	chr5:75901200-75911200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr5:75901200-75917000	Weak transcription	HUVEC	blood vessel
34	chr5:75901400-75903400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr5:75901400-75904000	Strong transcription	HepG2	liver
36	chr5:75901400-75912400	Weak transcription	Fetal Intestine Large	intestine
37	chr5:75901600-75907600	Weak transcription	Fetal Intestine Small	intestine
38	chr5:75902200-75903800	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr5:75902200-75905200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr5:75902400-75904400	Strong transcription	Placenta	Placenta
41	chr5:75902400-75905000	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr5:75902400-75905200	Genic enhancers	Primary B cells from cord blood	blood
43	chr5:75902600-75903400	Strong transcription	Gastric	stomach
44	chr5:75902600-75903600	Flanking Active TSS	NHDF-Ad	bronchial
45	chr5:75902600-75903800	Active TSS	Primary B cells from peripheral blood	blood
46	chr5:75902600-75903800	Enhancers	Fetal Kidney	kidney
47	chr5:75902600-75903800	Enhancers	Rectal Smooth Muscle	rectum
48	chr5:75902600-75904000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr5:75902600-75904000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr5:75902600-75919200	Strong transcription	Primary T cells from cord blood	blood

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