Variant report

Variant	rs10072221
Chromosome Location	chr5:75720544-75720545
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:75717306..75720750-chr5:75722224..75725340,4	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10043040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10044351	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10044370	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10044373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10065322	0.91[EUR][1000 genomes]
rs10068074	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10068404	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10068651	0.96[CEU][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10070688	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10073228	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10073282	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10073382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10073448	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10077372	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10079393	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10213849	0.96[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10462539	0.89[EUR][1000 genomes]
rs10462540	0.90[EUR][1000 genomes]
rs11738470	0.89[EUR][1000 genomes]
rs11740038	0.85[CEU][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs11741153	0.82[CHD][hapmap]
rs11743541	0.96[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11744637	0.91[EUR][1000 genomes]
rs11747990	0.91[EUR][1000 genomes]
rs11749318	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12523532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13175420	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13357820	0.89[EUR][1000 genomes]
rs28386181	0.90[EUR][1000 genomes]
rs3886042	0.90[EUR][1000 genomes]
rs3886043	0.85[CEU][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs4254886	0.91[EUR][1000 genomes]
rs4615280	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55995866	0.90[EUR][1000 genomes]
rs56189196	0.88[EUR][1000 genomes]
rs59428516	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60570368	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453217	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs6865628	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6887962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6895725	0.89[EUR][1000 genomes]
rs7706078	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7706926	0.85[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs7707426	0.91[EUR][1000 genomes]
rs7718641	0.91[EUR][1000 genomes]
rs7731240	0.91[EUR][1000 genomes]

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
rs10072221	IQGAP2	cis	multi-tissue	Pritchard

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75701000-75721600	Weak transcription	Fetal Stomach	stomach
2	chr5:75703000-75731800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr5:75703600-75747000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:75707000-75727600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr5:75709800-75727200	Weak transcription	Primary B cells from cord blood	blood
6	chr5:75710200-75720600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr5:75710200-75720800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr5:75711000-75733600	Weak transcription	Thymus	Thymus
9	chr5:75712400-75720600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:75717400-75720800	Weak transcription	Gastric	stomach
11	chr5:75717400-75722400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:75718000-75722600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:75718200-75720600	Weak transcription	Pancreas	Pancrea
14	chr5:75718400-75720600	Weak transcription	Primary T cells from cord blood	blood
15	chr5:75718400-75721600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr5:75718400-75725800	Weak transcription	HepG2	liver
17	chr5:75718600-75720600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr5:75718600-75720600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr5:75718600-75720600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr5:75718600-75720800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr5:75718600-75721600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:75718600-75722000	Weak transcription	Brain Germinal Matrix	brain
23	chr5:75718600-75722000	Weak transcription	Stomach Mucosa	stomach
24	chr5:75718600-75722400	Weak transcription	Fetal Intestine Small	intestine
25	chr5:75718600-75723600	Weak transcription	Small Intestine	intestine
26	chr5:75718800-75720600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr5:75718800-75720600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr5:75718800-75720800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr5:75718800-75721600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr5:75719000-75720600	Weak transcription	Fetal Kidney	kidney
31	chr5:75719000-75720600	Weak transcription	Fetal Lung	lung
32	chr5:75719200-75724800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr5:75719400-75721800	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr5:75719400-75722400	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr5:75719800-75720600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr5:75719800-75720600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr5:75719800-75720600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr5:75719800-75720800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:75719800-75721200	Weak transcription	Fetal Brain Female	brain
40	chr5:75719800-75722000	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr5:75720200-75721600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr5:75720200-75721800	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr5:75720200-75722000	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr5:75720200-75722400	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr5:75720400-75720800	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr5:75720400-75721200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
47	chr5:75720400-75722000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr5:75720400-75722800	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr5:75720400-75722800	Enhancers	Primary T cells fromperipheralblood	blood
50	chr5:75720400-75722800	Enhancers	Liver	Liver

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