Variant report

Variant	rs7099668
Chromosome Location	chr10:91107382-91107383
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	PAX5	chr10:91107365-91107886	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
LIPA	TF binding region

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10159512	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10159516	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10159652	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10159694	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10159869	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10159879	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1041540	0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs11203074	0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11203075	1.00[CEU][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11203076	0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11203077	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11203081	1.00[CEU][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11203084	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11203085	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11203087	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11203088	1.00[ASN][1000 genomes]
rs11203097	1.00[ASN][1000 genomes]
rs12241343	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12242568	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12244506	0.85[AMR][1000 genomes]
rs12244571	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12245627	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249661	1.00[ASN][1000 genomes]
rs12249707	1.00[ASN][1000 genomes]
rs12250753	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12250860	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12251895	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12256980	0.85[AFR][1000 genomes]
rs12259713	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12259768	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12261273	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12263989	1.00[ASN][1000 genomes]
rs12264051	1.00[ASN][1000 genomes]
rs12266581	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[LWK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12267943	1.00[ASN][1000 genomes]
rs1332332	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1332333	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1332334	0.91[ASW][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1332336	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1332337	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119593	1.00[CEU][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119665	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119672	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119790	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119791	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2151008	1.00[ASN][1000 genomes]
rs41284140	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41284142	1.00[ASN][1000 genomes]
rs4378299	1.00[ASN][1000 genomes]
rs6586185	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6586186	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6586187	0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6586189	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6586190	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6586191	1.00[CHD][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs7081163	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7088379	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7091558	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100115	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367441	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73367444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367460	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73368528	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7898580	0.80[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7901862	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7902096	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7902109	1.00[CEU][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7902380	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7904924	0.91[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7906827	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7907230	0.91[ASW][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs7907341	1.00[CEU][hapmap];0.88[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7911396	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7913002	0.85[TSI][hapmap]
rs7916398	1.00[CEU][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7917725	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9663337	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9663529	0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9663533	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv1041964	chr10:90861380-91378356	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv1040375	chr10:91022218-91153074	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	esv34085	chr10:91065949-91174175	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7099668	FCER2	trans	brain	seeQTL
rs7099668	GRK5	trans	brain	seeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91090200-91107600	Weak transcription	Pancreas	Pancrea
2	chr10:91094000-91110200	Weak transcription	Colonic Mucosa	Colon
3	chr10:91094000-91112000	Weak transcription	Esophagus	oesophagus
4	chr10:91094200-91108400	Weak transcription	Stomach Mucosa	stomach
5	chr10:91095200-91110400	Weak transcription	Colon Smooth Muscle	Colon
6	chr10:91097600-91107400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr10:91097600-91107400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr10:91098800-91111200	Weak transcription	Aorta	Aorta
9	chr10:91099400-91107800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr10:91099400-91111000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr10:91099600-91110400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr10:91099600-91110800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr10:91099800-91110400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr10:91099800-91111000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr10:91100000-91107400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr10:91100000-91107600	Weak transcription	Fetal Thymus	thymus
17	chr10:91100000-91110400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr10:91100000-91111000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr10:91100600-91110400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr10:91101200-91107400	Weak transcription	Lung	lung
21	chr10:91101200-91110000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr10:91101200-91111200	Weak transcription	Ovary	ovary
23	chr10:91101600-91110800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr10:91102600-91110400	Weak transcription	NH-A	brain
25	chr10:91102800-91110400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr10:91104000-91107600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr10:91104200-91107600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr10:91105000-91112400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr10:91105400-91108000	Enhancers	Hela-S3	cervix
30	chr10:91105400-91108400	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr10:91105400-91109000	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr10:91105400-91109000	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr10:91105400-91109000	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr10:91105400-91109200	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr10:91105400-91109400	Enhancers	HepG2	liver
36	chr10:91105400-91109800	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr10:91105600-91108200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr10:91105600-91108600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr10:91105600-91109400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr10:91105600-91109600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr10:91105600-91111200	Enhancers	Liver	Liver
42	chr10:91105600-91111200	Enhancers	Fetal Intestine Small	intestine
43	chr10:91105600-91111400	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr10:91105600-91112400	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr10:91105800-91113200	Enhancers	Fetal Intestine Large	intestine
46	chr10:91106000-91108200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr10:91106000-91108200	Enhancers	Muscle Satellite Cultured Cells	--
48	chr10:91106000-91108200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr10:91106000-91108800	Enhancers	NHDF-Ad	bronchial
50	chr10:91106000-91109000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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