Variant report

Variant	rs1859690
Chromosome Location	chr7:99227172-99227173
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99221268..99223879-chr7:99225955..99229259,4	MCF-7	breast:
2	chr7:99174028..99175848-chr7:99226635..99229515,2	K562	blood:
3	chr7:99226925..99228717-chr7:99515670..99518540,2	K562	blood:
4	chr7:99226823..99229371-chr7:99278363..99279988,2	K562	blood:

Variant related genes	Relation type
ENSG00000146833	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10211	0.94[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10225314	0.80[JPT][hapmap]
rs10227637	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10229552	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10238028	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10238965	0.83[JPT][hapmap]
rs10242455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10254729	0.83[JPT][hapmap]
rs10258552	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10282706	0.94[ASW][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11772470	0.83[JPT][hapmap]
rs12333599	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12334072	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12334077	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12360	0.95[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13362853	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1357319	0.95[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs1403196	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1419745	0.90[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.80[ASN][1000 genomes]
rs15524	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17161774	0.90[CHB][hapmap]
rs17161780	0.85[CHB][hapmap]
rs17161783	0.90[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs1818797	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1851425	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1879859	0.94[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2037497	0.82[ASN][1000 genomes]
rs2037498	0.95[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs2037499	0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2090949	0.82[ASN][1000 genomes]
rs2140128	0.82[ASN][1000 genomes]
rs2177180	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2222411	0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs2257401	0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs2404769	0.82[ASN][1000 genomes]
rs2404770	0.95[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2687072	0.82[ASN][1000 genomes]
rs2687075	0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs2687076	0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs2687077	0.85[ASN][1000 genomes]
rs2687078	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2687079	0.94[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2687081	0.94[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2687084	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2687085	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2687086	0.95[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2687087	0.94[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2687133	0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2687134	0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.80[ASN][1000 genomes]
rs2687135	0.82[ASN][1000 genomes]
rs2687136	0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs2687137	0.82[ASN][1000 genomes]
rs2687139	0.95[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2687140	0.87[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2687141	0.82[ASN][1000 genomes]
rs2687142	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.82[ASN][1000 genomes]
rs2687143	0.82[ASN][1000 genomes]
rs2687144	0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2687145	0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs2740558	0.82[ASN][1000 genomes]
rs2740559	0.82[ASN][1000 genomes]
rs2740560	0.82[ASN][1000 genomes]
rs2740561	0.95[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2740562	0.81[ASN][1000 genomes]
rs2740563	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2740565	0.94[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2741872	0.80[ASN][1000 genomes]
rs2948343	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2948344	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3735453	0.94[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3779354	1.00[CEU][hapmap]
rs3800960	0.83[JPT][hapmap]
rs45624139	0.82[ASN][1000 genomes]
rs4646446	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs4646447	0.90[CHB][hapmap];0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs4646449	0.90[CHB][hapmap];0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs4646450	0.95[CHB][hapmap];0.90[CHD][hapmap];0.89[ASN][1000 genomes]
rs4646453	0.90[CHB][hapmap];0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs4646456	0.90[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4646457	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4646458	0.90[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4646461	0.80[ASN][1000 genomes]
rs4646465	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs55852703	0.82[ASN][1000 genomes]
rs58024720	0.80[ASN][1000 genomes]
rs58649180	0.80[ASN][1000 genomes]
rs61337492	0.84[ASN][1000 genomes]
rs6465750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6961634	0.83[JPT][hapmap]
rs72494455	0.80[ASN][1000 genomes]
rs73410654	0.82[ASN][1000 genomes]
rs776741	0.85[CHB][hapmap]
rs776742	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs776744	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs776745	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs776746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7780328	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7808022	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[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];0.97[ASN][1000 genomes]
rs868564	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9769359	0.95[AMR][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	nsv482532	chr7:99205906-99363886	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv981815	chr7:99224245-99235459	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1859690	CYP3A5	cis	normal skin	skin_eQTL
rs1859690	BUD31	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99215000-99236000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:99215800-99229400	Strong transcription	Fetal Muscle Leg	muscle
3	chr7:99215800-99229600	Weak transcription	Right Atrium	heart
4	chr7:99215800-99231800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:99215800-99232200	Strong transcription	Fetal Stomach	stomach
6	chr7:99216000-99228800	Strong transcription	Skeletal Muscle Male	skeletal muscle
7	chr7:99216000-99229000	Strong transcription	K562	blood
8	chr7:99216000-99229400	Strong transcription	Fetal Lung	lung
9	chr7:99216000-99231400	Strong transcription	Brain Inferior Temporal Lobe	brain
10	chr7:99216200-99228200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr7:99216200-99229400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr7:99216200-99229400	Strong transcription	Left Ventricle	heart
13	chr7:99216200-99229800	Strong transcription	H9 Cell Line	embryonic stem cell
14	chr7:99216200-99230200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr7:99216200-99230400	Strong transcription	NHLF	lung
16	chr7:99216200-99230600	Strong transcription	Adipose Nuclei	Adipose
17	chr7:99216200-99231800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr7:99216200-99231800	Strong transcription	Placenta	Placenta
19	chr7:99216200-99231800	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr7:99216200-99232000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:99216200-99232000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:99216200-99232000	Strong transcription	Fetal Intestine Large	intestine
23	chr7:99216200-99232200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr7:99216200-99232200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr7:99216200-99232200	Strong transcription	Lung	lung
26	chr7:99216400-99228000	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr7:99216400-99228200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr7:99216400-99228400	Strong transcription	Colon Smooth Muscle	Colon
29	chr7:99216400-99228600	Strong transcription	HepG2	liver
30	chr7:99216400-99229200	Strong transcription	Brain Cingulate Gyrus	brain
31	chr7:99216400-99229200	Strong transcription	Brain Hippocampus Middle	brain
32	chr7:99216400-99229200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr7:99216400-99229200	Strong transcription	A549	lung
34	chr7:99216400-99229400	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr7:99216400-99230600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr7:99216400-99231600	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr7:99216400-99231800	Strong transcription	Fetal Brain Female	brain
38	chr7:99216400-99232000	Strong transcription	Primary B cells from cord blood	blood
39	chr7:99216400-99232000	Strong transcription	GM12878-XiMat	blood
40	chr7:99216400-99232400	Strong transcription	Brain Germinal Matrix	brain
41	chr7:99216600-99228400	Strong transcription	Primary hematopoietic stem cells	blood
42	chr7:99216600-99228600	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr7:99216600-99229200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr7:99216600-99229200	Strong transcription	Brain Angular Gyrus	brain
45	chr7:99216600-99229400	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr7:99216600-99229400	Strong transcription	Osteobl	bone
47	chr7:99216600-99230400	Strong transcription	Colonic Mucosa	Colon
48	chr7:99216600-99230400	Strong transcription	HUVEC	blood vessel
49	chr7:99216600-99230800	Strong transcription	Liver	Liver
50	chr7:99216600-99231800	Strong transcription	Brain Substantia Nigra	brain

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