Variant report

Variant	rs776746
Chromosome Location	chr7:99270539-99270540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99259676..99261606-chr7:99268360..99270829,2	MCF-7	breast:
2	chr7:99269970..99274089-chr7:99274560..99278506,7	MCF-7	breast:
3	chr7:99212976..99215779-chr7:99269486..99271923,2	K562	blood:

Variant related genes	Relation type
ENSG00000106258	Chromatin interaction
ENSG00000197037	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10211	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs10227637	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10229552	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10238028	0.85[AMR][1000 genomes]
rs10238965	0.84[JPT][hapmap]
rs10242455	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10254729	0.84[JPT][hapmap]
rs10258552	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10282706	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11772470	0.84[JPT][hapmap]
rs12333599	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12334072	0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12334077	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12360	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13362853	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1357319	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1403196	0.92[ASN][1000 genomes]
rs1419745	0.90[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs15524	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17161774	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs17161780	0.85[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs17161783	0.90[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs1818797	0.92[ASN][1000 genomes]
rs1851425	0.92[ASN][1000 genomes]
rs1859690	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]
rs1879859	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[ASN][1000 genomes]
rs2037497	0.88[ASN][1000 genomes]
rs2037498	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2037499	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2090949	0.88[ASN][1000 genomes]
rs2140128	0.88[ASN][1000 genomes]
rs2177180	0.92[ASN][1000 genomes]
rs2222411	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2257401	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2404769	0.88[ASN][1000 genomes]
rs2404770	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2687072	0.88[ASN][1000 genomes]
rs2687075	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2687076	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2687077	0.92[ASN][1000 genomes]
rs2687078	0.92[ASN][1000 genomes]
rs2687079	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs2687081	0.94[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[ASN][1000 genomes]
rs2687084	0.92[ASN][1000 genomes]
rs2687085	0.92[ASN][1000 genomes]
rs2687086	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2687087	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs2687133	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2687134	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2687135	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2687136	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2687137	0.88[ASN][1000 genomes]
rs2687139	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2687140	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2687141	0.88[ASN][1000 genomes]
rs2687142	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2687143	0.88[ASN][1000 genomes]
rs2687144	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2687145	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2740558	0.88[ASN][1000 genomes]
rs2740559	0.88[ASN][1000 genomes]
rs2740560	0.88[ASN][1000 genomes]
rs2740561	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2740562	0.88[ASN][1000 genomes]
rs2740563	0.90[ASN][1000 genomes]
rs2740565	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[ASN][1000 genomes]
rs2741872	0.87[ASN][1000 genomes]
rs2948343	0.92[ASN][1000 genomes]
rs2948344	0.92[ASN][1000 genomes]
rs3735453	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3800960	0.82[JPT][hapmap]
rs3823812	0.86[ASN][1000 genomes]
rs45624139	0.88[ASN][1000 genomes]
rs4646446	0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs4646447	0.90[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs4646449	0.90[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs4646450	0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs4646453	0.90[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs4646456	0.90[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs4646457	0.94[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4646458	0.90[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];0.83[ASN][1000 genomes]
rs4646461	0.87[ASN][1000 genomes]
rs4646465	0.92[ASN][1000 genomes]
rs55852703	0.88[ASN][1000 genomes]
rs58024720	0.87[ASN][1000 genomes]
rs58649180	0.87[ASN][1000 genomes]
rs60865030	0.83[ASN][1000 genomes]
rs6465750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6961634	0.84[JPT][hapmap]
rs72494453	0.81[ASN][1000 genomes]
rs72494455	0.87[ASN][1000 genomes]
rs73410654	0.88[ASN][1000 genomes]
rs776739	0.81[ASN][1000 genomes]
rs776741	0.85[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs776742	0.93[ASN][1000 genomes]
rs776744	0.93[ASN][1000 genomes]
rs776745	0.93[ASN][1000 genomes]
rs7780328	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7798931	0.85[ASN][1000 genomes]
rs7808022	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]
rs868564	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs9769359	0.83[AMR][1000 genomes];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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs776746	CYP3A5	cis	normal skin	skin_eQTL
rs776746	CYP3A5	cis	Liver	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99229200-99275000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr7:99229800-99272600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr7:99230400-99272000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr7:99232000-99275000	Weak transcription	A549	lung
5	chr7:99235800-99276400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:99237000-99272200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr7:99242400-99272400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr7:99243000-99278800	Weak transcription	Brain Angular Gyrus	brain
9	chr7:99243600-99276800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr7:99251600-99276400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:99254400-99275400	Weak transcription	Fetal Stomach	stomach
12	chr7:99255800-99277000	Weak transcription	Fetal Brain Male	brain
13	chr7:99257200-99274600	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr7:99257400-99274600	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr7:99257800-99271400	Weak transcription	Fetal Thymus	thymus
16	chr7:99258400-99276400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr7:99258600-99274400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr7:99258600-99274800	Weak transcription	Lung	lung
19	chr7:99258600-99276600	Weak transcription	Colon Smooth Muscle	Colon
20	chr7:99259000-99271800	Weak transcription	Ovary	ovary
21	chr7:99259200-99271800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr7:99260200-99277000	Weak transcription	Spleen	Spleen
23	chr7:99260600-99276600	Weak transcription	Adipose Nuclei	Adipose
24	chr7:99260600-99276800	Weak transcription	Left Ventricle	heart
25	chr7:99261200-99273600	Weak transcription	Gastric	stomach
26	chr7:99261200-99274400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr7:99261400-99272200	Weak transcription	Primary T cells from cord blood	blood
28	chr7:99261400-99277000	Weak transcription	Small Intestine	intestine
29	chr7:99262200-99272000	Strong transcription	Liver	Liver
30	chr7:99263400-99273000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr7:99263600-99277400	Weak transcription	Aorta	Aorta
32	chr7:99264400-99273400	Weak transcription	Stomach Mucosa	stomach
33	chr7:99264600-99270600	Weak transcription	Colonic Mucosa	Colon
34	chr7:99264600-99273400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr7:99267800-99272600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr7:99268000-99272400	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr7:99269000-99273000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr7:99269000-99276600	Weak transcription	HMEC	breast
39	chr7:99269200-99274200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr7:99269400-99270600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr7:99269600-99273400	Weak transcription	HepG2	liver
42	chr7:99270000-99270600	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr7:99270000-99271600	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr7:99270000-99272200	Strong transcription	Pancreas	Pancrea
45	chr7:99270200-99270600	Enhancers	K562	blood
46	chr7:99270200-99270600	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr7:99270200-99270800	Genic enhancers	Fetal Intestine Small	intestine
48	chr7:99270200-99271000	Strong transcription	Esophagus	oesophagus
49	chr7:99270200-99271600	Genic enhancers	Fetal Intestine Large	intestine
50	chr7:99270200-99272000	Strong transcription	Fetal Lung	lung

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