Variant report

Variant	rs7448
Chromosome Location	chr10:98353213-98353214
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:98345341..98350021-chr10:98351580..98356203,7	MCF-7	breast:
2	chr10:98352916..98354492-chr10:98357583..98359914,2	K562	blood:
3	chr10:98345273..98348471-chr10:98351958..98358343,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000077147	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10128106	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1018604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1018605	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051450	0.88[CHD][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs1063605	0.94[ASN][1000 genomes]
rs10736114	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10882809	0.82[ASN][1000 genomes]
rs10882811	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10882813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10882815	0.88[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs10882817	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10882821	0.88[ASN][1000 genomes]
rs10882822	0.81[AMR][1000 genomes]
rs10882826	0.87[CEU][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs10882827	0.81[ASN][1000 genomes]
rs10882828	0.90[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11188809	0.82[ASN][1000 genomes]
rs11188810	0.82[ASN][1000 genomes]
rs11188811	0.82[ASN][1000 genomes]
rs11188813	0.82[ASN][1000 genomes]
rs11188814	0.82[ASN][1000 genomes]
rs11188815	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs11188817	0.88[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs11188821	0.82[ASN][1000 genomes]
rs11188822	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs11188825	0.88[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs11188827	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11188831	0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs11188832	0.91[ASN][1000 genomes]
rs11188833	0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs11188840	0.91[ASN][1000 genomes]
rs11188842	0.94[ASN][1000 genomes]
rs11188844	0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs11188847	0.81[CHD][hapmap];0.84[ASN][1000 genomes]
rs11188848	0.87[ASN][1000 genomes]
rs11188853	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11188856	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs1132913	0.88[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs1132914	0.80[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs1156035	0.82[ASN][1000 genomes]
rs1156036	0.82[ASN][1000 genomes]
rs11814010	0.82[ASN][1000 genomes]
rs12218847	0.82[ASN][1000 genomes]
rs12219275	0.84[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs12220047	0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs12221143	0.82[ASN][1000 genomes]
rs12221262	0.82[ASN][1000 genomes]
rs12414612	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs12415048	0.82[ASN][1000 genomes]
rs12416646	0.84[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs12761817	0.82[ASN][1000 genomes]
rs12766248	0.82[ASN][1000 genomes]
rs12775533	0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs12776810	0.94[ASN][1000 genomes]
rs12779720	0.88[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1324255	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs1324256	0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs1324258	1.00[CEU][hapmap]
rs1324259	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1324261	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1408367	0.88[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs17391547	0.82[ASN][1000 genomes]
rs17482382	0.82[ASN][1000 genomes]
rs1983831	0.92[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs2011190	0.82[ASN][1000 genomes]
rs2025451	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2031326	0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs2031329	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2861555	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs33964467	0.88[CHD][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs35779764	0.88[CHD][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs36098523	0.87[ASN][1000 genomes]
rs3689	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs3748234	1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs3748235	0.83[ASW][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap]
rs3748236	0.85[ASN][1000 genomes]
rs3748237	0.94[ASN][1000 genomes]
rs3789957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3789958	0.82[ASN][1000 genomes]
rs3818389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4146727	0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs4485036	0.84[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4534508	0.88[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4917742	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4919029	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4919032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4919037	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4919040	0.80[CEU][hapmap];0.85[CHB][hapmap]
rs58305369	0.87[ASN][1000 genomes]
rs61858194	0.88[ASN][1000 genomes]
rs61858494	0.82[ASN][1000 genomes]
rs61859300	0.94[ASN][1000 genomes]
rs7069429	0.85[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs7070686	0.94[ASN][1000 genomes]
rs7071044	0.88[CHD][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs7071224	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs7071881	0.94[ASN][1000 genomes]
rs7073017	0.87[ASN][1000 genomes]
rs7073682	0.87[ASN][1000 genomes]
rs7074516	0.88[CHD][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs7082873	0.91[ASN][1000 genomes]
rs7085389	0.94[ASN][1000 genomes]
rs7086213	0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs7086240	0.82[ASN][1000 genomes]
rs7087478	0.82[ASN][1000 genomes]
rs7091606	0.88[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs7097291	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101320	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs713251	0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs727329	0.82[ASN][1000 genomes]
rs7914154	1.00[JPT][hapmap];0.91[MEX][hapmap]
rs7919739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8578	0.88[CHD][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs912480	0.87[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs927639	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9633703	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9664749	0.88[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs9664955	0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413353	chr10:98039370-98561524	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7448	PIK3AP1	cis	Liver	GTEx
rs7448	LCOR	cis	multi-tissue	Pritchard
rs7448	TM9SF3	cis	parietal	SCAN
rs7448	PIK3AP1	cis	multi-tissue	Pritchard
rs7448	NPM1P26	cis	Stomach	GTEx
rs7448	TM9SF3	cis	Liver	GTEx
rs7448	TM9SF3	cis	Thyroid	GTEx
rs7448	NPM1P26	cis	Adipose Subcutaneous	GTEx
rs7448	NPM1P26	cis	Esophagus Muscularis	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98347000-98354600	Weak transcription	Spleen	Spleen
2	chr10:98347400-98358800	Weak transcription	Pancreas	Pancrea
3	chr10:98347800-98365800	Weak transcription	Ovary	ovary
4	chr10:98348000-98354600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr10:98348000-98373600	Weak transcription	Left Ventricle	heart
6	chr10:98348200-98354200	Weak transcription	Placenta	Placenta
7	chr10:98348200-98356200	Weak transcription	Adipose Nuclei	Adipose
8	chr10:98348200-98357800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr10:98348200-98359000	Weak transcription	Brain Substantia Nigra	brain
10	chr10:98348800-98355200	Weak transcription	HSMMtube	muscle
11	chr10:98349600-98354800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr10:98349600-98355600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr10:98349800-98354200	Weak transcription	Fetal Intestine Large	intestine
14	chr10:98349800-98354400	Weak transcription	Fetal Intestine Small	intestine
15	chr10:98349800-98354400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr10:98349800-98355200	Weak transcription	K562	blood
17	chr10:98349800-98366400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr10:98349800-98367800	Weak transcription	Small Intestine	intestine
19	chr10:98350000-98355200	Weak transcription	Stomach Mucosa	stomach
20	chr10:98350800-98395600	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr10:98351600-98363400	Weak transcription	Brain Hippocampus Middle	brain
22	chr10:98352400-98353600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr10:98352400-98357200	Strong transcription	GM12878-XiMat	blood
24	chr10:98352400-98378600	Strong transcription	Liver	Liver
25	chr10:98352400-98399400	Strong transcription	Primary B cells from peripheral blood	blood
26	chr10:98352600-98369400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr10:98352600-98403000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr10:98352800-98353800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr10:98352800-98354200	Strong transcription	Primary B cells from cord blood	blood
30	chr10:98352800-98354800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
31	chr10:98353000-98388400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr10:98353000-98403000	Strong transcription	Primary monocytes fromperipheralblood	blood

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