Variant report

Variant	rs3886043
Chromosome Location	chr5:75704085-75704086
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	chr5:75697502..75699104-chr5:75703353..75706054,2	K562	blood:

Variant related genes	Relation type
ENSG00000145703	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10043040	0.90[EUR][1000 genomes]
rs10044351	0.90[EUR][1000 genomes]
rs10044370	0.85[CEU][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs10044373	0.90[EUR][1000 genomes]
rs10065322	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10068074	0.90[EUR][1000 genomes]
rs10068404	0.83[EUR][1000 genomes]
rs10068651	0.89[CEU][hapmap]
rs10070688	0.90[EUR][1000 genomes]
rs10072221	0.85[CEU][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs10073228	0.90[EUR][1000 genomes]
rs10073282	0.90[EUR][1000 genomes]
rs10073382	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs10073448	0.92[EUR][1000 genomes]
rs10075621	0.84[JPT][hapmap]
rs10077372	0.85[CEU][hapmap];0.84[MEX][hapmap];0.90[EUR][1000 genomes]
rs10079393	0.89[EUR][1000 genomes]
rs10213849	0.89[CEU][hapmap]
rs10462539	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10462540	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1122654	0.80[ASN][1000 genomes]
rs11738470	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11740038	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11743541	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs11744637	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11747990	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11749318	0.85[CEU][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes]
rs12523532	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs13175420	0.91[EUR][1000 genomes]
rs13357820	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1984636	0.82[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs28386181	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3886042	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3951318	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs4254886	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4296785	0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs4501323	0.88[ASN][1000 genomes]
rs4501324	0.88[ASN][1000 genomes]
rs4615280	0.90[EUR][1000 genomes]
rs4704310	0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs55995866	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56189196	0.90[EUR][1000 genomes]
rs57929471	0.83[ASN][1000 genomes]
rs59428516	0.89[EUR][1000 genomes]
rs60570368	0.90[EUR][1000 genomes]
rs62363210	0.84[ASN][1000 genomes]
rs6453217	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6865628	0.85[CEU][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs6887962	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs6895725	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7706926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7707426	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7718641	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7731240	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs875541	0.81[JPT][hapmap]
rs875543	0.82[CHD][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv882206	chr5:75676658-75746813	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3886043	IQGAP2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75700200-75704600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr5:75700600-75707400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:75700800-75707200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:75701000-75706200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr5:75701000-75721600	Weak transcription	Fetal Stomach	stomach
6	chr5:75701200-75704400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr5:75701200-75704400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr5:75701200-75706800	Enhancers	Primary T cells fromperipheralblood	blood
9	chr5:75701400-75705400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:75701600-75707200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr5:75701600-75707200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr5:75701600-75713000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:75701800-75704400	Enhancers	Stomach Mucosa	stomach
14	chr5:75701800-75705800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr5:75701800-75706600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr5:75701800-75707000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:75702000-75704800	Enhancers	Placenta	Placenta
18	chr5:75702000-75706400	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr5:75702000-75707800	Enhancers	HepG2	liver
20	chr5:75702200-75704400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr5:75702200-75705400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr5:75702200-75707800	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr5:75702400-75705400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr5:75702600-75704200	Weak transcription	Fetal Intestine Small	intestine
25	chr5:75702600-75704400	Enhancers	Liver	Liver
26	chr5:75702600-75706200	Enhancers	Primary hematopoietic stem cells	blood
27	chr5:75702600-75707200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr5:75702800-75704400	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr5:75702800-75704400	Enhancers	Pancreas	Pancrea
30	chr5:75703000-75731800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr5:75703200-75704400	Weak transcription	Primary B cells from peripheral blood	blood
32	chr5:75703200-75704400	Weak transcription	Adipose Nuclei	Adipose
33	chr5:75703200-75706800	Weak transcription	Gastric	stomach
34	chr5:75703200-75717800	Weak transcription	Small Intestine	intestine
35	chr5:75703400-75704200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr5:75703400-75704400	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr5:75703400-75705600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr5:75703400-75715600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr5:75703400-75718000	Weak transcription	Primary T cells from cord blood	blood
40	chr5:75703600-75704200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr5:75703600-75704400	Enhancers	GM12878-XiMat	blood
42	chr5:75703600-75705600	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr5:75703600-75747000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr5:75703800-75709000	Weak transcription	Primary B cells from cord blood	blood
45	chr5:75703800-75709400	Weak transcription	Duodenum Mucosa	Duodenum

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