Variant report

Variant	rs16873476
Chromosome Location	chr5:75840039-75840040
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	EBF1	chr5:75839964-75840457	GM12878	blood:	n/a	chr5:75840109-75840120
2	STAT3	chr5:75840027-75840066	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr5:75838483-75840557	PBDE	blood:	n/a	n/a
4	WRNIP1	chr5:75839886-75840432	GM12878	blood:	n/a	n/a
5	MAZ	chr5:75839888-75840381	HepG2	liver:	n/a	chr5:75839967-75839976
6	SMC3	chr5:75839628-75840700	SK-N-SH	brain:	n/a	chr5:75840325-75840339
7	RAD21	chr5:75839999-75840617	MCF-7	breast:	n/a	chr5:75840321-75840340
8	CTCF	chr5:75840029-75840689	HCT-116	colon:	n/a	chr5:75840111-75840120 chr5:75840318-75840339
9	RAD21	chr5:75839690-75840758	SK-N-SH	brain:	n/a	chr5:75840321-75840340
10	CTCF	chr5:75839813-75840696	SK-N-SH	brain:	n/a	chr5:75840111-75840120 chr5:75840318-75840339
11	CTCF	chr5:75839606-75840679	A549	lung:	n/a	chr5:75840111-75840120 chr5:75840318-75840339
12	CTCF	chr5:75839900-75840050	GM12873	blood:	n/a	n/a
13	RAD21	chr5:75840029-75840603	HCT-116	colon:	n/a	chr5:75840321-75840340
14	RAD21	chr5:75840031-75840637	HCT-116	colon:	n/a	chr5:75840321-75840340
15	EBF1	chr5:75839945-75840299	GM12878	blood:	n/a	chr5:75840109-75840120
16	RAD21	chr5:75839986-75840582	HepG2	liver:	n/a	chr5:75840321-75840340
17	RAD21	chr5:75839893-75840565	H1-hESC	embryonic stem cell:	n/a	chr5:75840321-75840340
18	RAD21	chr5:75840008-75840534	SK-N-SH_RA	brain:	n/a	chr5:75840321-75840340

No.	Distal block	Cell Line	Cell type
1	chr5:75698659..75699503-chr5:75839829..75840376,2	K562	blood:
2	chr5:75628819..75631136-chr5:75840007..75842103,2	K562	blood:
3	chr5:75633886..75634436-chr5:75839825..75840735,2	K562	blood:
4	chr5:75698517..75699563-chr5:75839811..75840781,6	MCF-7	breast:
5	chr5:75633417..75634381-chr5:75839891..75840630,3	MCF-7	breast:
6	chr5:75633462..75634419-chr5:75839412..75840924,7	MCF-7	breast:

Variant related genes	Relation type
IQGAP2	TF binding region
ENSG00000145703	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11948140	0.85[CEU][hapmap];0.91[ASN][1000 genomes]
rs11951829	0.91[ASN][1000 genomes]
rs11952193	0.91[ASN][1000 genomes]
rs11952962	0.85[CEU][hapmap];0.91[ASN][1000 genomes]
rs1393098	0.85[CEU][hapmap];0.85[CHD][hapmap];0.91[ASN][1000 genomes]
rs1501689	0.91[ASN][1000 genomes]
rs16873461	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16873483	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16873519	1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs2005247	0.91[ASN][1000 genomes]
rs3736395	1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs3913473	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3913474	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3913475	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703712	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs4704327	0.91[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4704328	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4704334	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4704335	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704337	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704341	0.85[CEU][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs4704342	0.91[ASN][1000 genomes]
rs4704343	0.91[ASN][1000 genomes]
rs4704344	0.85[CEU][hapmap];0.91[ASN][1000 genomes]
rs58542602	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62361989	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62361990	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62361991	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62361992	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62361993	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62361994	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62361997	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362011	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362012	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362013	1.00[ASN][1000 genomes]
rs62362014	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362016	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362017	0.95[ASN][1000 genomes]
rs62362019	0.91[ASN][1000 genomes]
rs62362020	0.91[ASN][1000 genomes]
rs62362022	0.91[ASN][1000 genomes]
rs62362035	0.91[ASN][1000 genomes]
rs62362036	0.91[ASN][1000 genomes]
rs62362037	0.91[ASN][1000 genomes]
rs62362038	0.91[ASN][1000 genomes]
rs62362039	0.91[ASN][1000 genomes]
rs62362043	0.91[ASN][1000 genomes]
rs72775801	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72777503	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72777520	0.91[ASN][1000 genomes]
rs72777522	0.91[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
rs16873476	IQGAP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75830000-75841600	Enhancers	Stomach Mucosa	stomach
2	chr5:75835600-75871200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:75837400-75840600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr5:75837400-75842800	Enhancers	Liver	Liver
5	chr5:75837800-75840600	Enhancers	Fetal Lung	lung
6	chr5:75837800-75841200	Enhancers	Placenta	Placenta
7	chr5:75838000-75840400	Enhancers	Fetal Thymus	thymus
8	chr5:75838000-75840600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:75838200-75840200	Enhancers	Small Intestine	intestine
10	chr5:75838200-75840600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr5:75838200-75841400	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr5:75838400-75840200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr5:75838400-75840200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr5:75838400-75840600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr5:75838400-75840600	Enhancers	Fetal Kidney	kidney
16	chr5:75838600-75840200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr5:75838600-75840400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr5:75838600-75840400	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr5:75838600-75840600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr5:75838800-75840200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr5:75838800-75840200	Enhancers	Gastric	stomach
22	chr5:75839000-75840200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr5:75839000-75840400	Enhancers	H1 Cell Line	embryonic stem cell
24	chr5:75839000-75840400	Enhancers	Lung	lung
25	chr5:75839000-75840600	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr5:75839000-75840600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:75839000-75841600	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr5:75839200-75840200	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr5:75839200-75840600	Enhancers	Pancreas	Pancrea
30	chr5:75839200-75840800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr5:75839200-75841400	Enhancers	Fetal Intestine Small	intestine
32	chr5:75839400-75840200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr5:75839400-75840200	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr5:75839400-75840400	Enhancers	Primary B cells from peripheral blood	blood
35	chr5:75839400-75840400	Enhancers	Fetal Intestine Large	intestine
36	chr5:75839400-75840600	Enhancers	Primary B cells from cord blood	blood
37	chr5:75839400-75840600	Enhancers	Primary T cells from cord blood	blood
38	chr5:75839400-75840600	Enhancers	K562	blood
39	chr5:75839400-75840600	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr5:75839400-75842200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:75839400-75842400	Weak transcription	Adipose Nuclei	Adipose
42	chr5:75839400-75842600	Weak transcription	Thymus	Thymus
43	chr5:75839600-75840400	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr5:75839600-75845400	Enhancers	HepG2	liver
45	chr5:75839600-75845800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr5:75839600-75846000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr5:75839800-75840200	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr5:75839800-75840200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr5:75839800-75840200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr5:75839800-75840200	Enhancers	Colonic Mucosa	Colon

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