Variant report

Variant	rs16873461
Chromosome Location	chr5:75834448-75834449
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs16873476	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	1.00[CHB][hapmap];0.95[MKK][hapmap]
rs3736395	0.81[MKK][hapmap]
rs3913474	0.81[EUR][1000 genomes]
rs3913475	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs4703712	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[TSI][hapmap]
rs4704327	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4704328	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4704334	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4704335	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58542602	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62361989	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62361990	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62361991	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62361992	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62361993	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62361994	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62361997	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72775801	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72777503	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16873461	IQGAP2	Cis_1M	lymphoblastoid	RTeQTL
rs16873461	COX6A2	trans	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75806800-75839200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:75823000-75838400	Weak transcription	Primary T cells from cord blood	blood
3	chr5:75826600-75834800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:75826800-75834600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr5:75826800-75840000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr5:75827000-75835000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr5:75828600-75839000	Weak transcription	Lung	lung
8	chr5:75829000-75836200	Weak transcription	K562	blood
9	chr5:75829000-75838000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr5:75830000-75841600	Enhancers	Stomach Mucosa	stomach
11	chr5:75831600-75834600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr5:75831600-75834600	Weak transcription	Gastric	stomach
13	chr5:75831600-75834800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:75831800-75836400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:75831800-75837400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr5:75832200-75839000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr5:75832200-75840000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr5:75832400-75836600	Enhancers	Placenta	Placenta
19	chr5:75832400-75838600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr5:75832600-75838400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:75833200-75838600	Enhancers	Duodenum Mucosa	Duodenum
22	chr5:75833400-75836600	Enhancers	Pancreas	Pancrea
23	chr5:75833400-75838400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:75833400-75838800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr5:75833600-75837000	Enhancers	Liver	Liver
26	chr5:75833600-75839800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr5:75833800-75837800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr5:75833800-75838200	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr5:75833800-75838600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr5:75833800-75838600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr5:75834000-75834800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr5:75834000-75835200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr5:75834000-75835600	Enhancers	Primary T cells fromperipheralblood	blood
34	chr5:75834000-75836000	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr5:75834000-75836600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr5:75834000-75836600	Enhancers	HepG2	liver
37	chr5:75834000-75838200	Weak transcription	Small Intestine	intestine
38	chr5:75834000-75839200	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr5:75834200-75839000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr5:75834200-75839000	Enhancers	Primary hematopoietic stem cells	blood
41	chr5:75834200-75839200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:75834400-75834800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr5:75834400-75835000	Enhancers	Fetal Thymus	thymus
44	chr5:75834400-75835600	Enhancers	Spleen	Spleen
45	chr5:75834400-75839200	Weak transcription	Fetal Intestine Small	intestine

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