Variant report

Variant	rs4646446
Chromosome Location	chr7:99275083-99275084
allele	A/G
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	TAL1	chr7:99275040-99275118	K562	blood:	n/a	n/a
2	FOXA2	chr7:99274937-99275601	HepG2	liver:	n/a	n/a
3	FOXA2	chr7:99274978-99275885	HepG2	liver:	n/a	n/a
4	MAX	chr7:99274832-99275783	HepG2	liver:	n/a	n/a
5	FOXA1	chr7:99274954-99275662	HepG2	liver:	n/a	n/a
6	ARID3A	chr7:99275040-99275588	HepG2	liver:	n/a	n/a
7	FOXA1	chr7:99274800-99275682	HepG2	liver:	n/a	n/a
8	NR2F2	chr7:99274980-99275757	HepG2	liver:	n/a	n/a
9	FOXA1	chr7:99275041-99275707	HepG2	liver:	n/a	n/a
10	MAX	chr7:99275082-99275692	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:99274008..99275570-chr7:99277098..99278652,2	K562	blood:

Variant related genes	Relation type
CYP3A5	TF binding region
ENSG00000106258	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10211	0.90[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs10225314	0.86[JPT][hapmap];0.92[EUR][1000 genomes]
rs10229552	0.82[ASN][1000 genomes]
rs10242455	0.85[CHB][hapmap];0.81[CHD][hapmap];0.82[ASN][1000 genomes]
rs10282706	0.80[CHB][hapmap];0.80[CHD][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs10464604	0.92[EUR][1000 genomes]
rs11539770	0.92[EUR][1000 genomes]
rs12334077	0.81[ASN][1000 genomes]
rs12360	0.90[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs13362853	0.80[ASN][1000 genomes]
rs1357319	0.90[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap]
rs1403196	0.81[ASN][1000 genomes]
rs1419745	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs15524	0.85[CHB][hapmap];0.81[CHD][hapmap];0.82[ASN][1000 genomes]
rs17161766	0.84[EUR][1000 genomes]
rs17161768	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17161769	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17161771	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17161772	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17161774	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17161780	0.90[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17161783	1.00[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1818797	0.81[ASN][1000 genomes]
rs1851425	0.81[ASN][1000 genomes]
rs1851427	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1859690	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs1879859	0.90[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2005548	0.83[ASN][1000 genomes]
rs2037498	0.90[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap]
rs2037499	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2177180	0.81[ASN][1000 genomes]
rs2222411	0.90[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap]
rs2257401	0.90[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2404770	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2687075	0.90[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap]
rs2687076	0.90[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2687077	0.81[ASN][1000 genomes]
rs2687078	0.81[ASN][1000 genomes]
rs2687079	0.90[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2687081	0.83[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2687084	0.81[ASN][1000 genomes]
rs2687085	0.81[ASN][1000 genomes]
rs2687086	0.90[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2687087	0.90[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2687133	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2687134	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap]
rs2687136	0.90[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap]
rs2687139	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2687140	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs2687142	0.90[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap]
rs2687144	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2687145	0.90[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap]
rs2740561	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs2740565	0.90[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2948343	0.81[ASN][1000 genomes]
rs2948344	0.81[ASN][1000 genomes]
rs3735453	0.85[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs3800960	0.82[ASW][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3823812	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41301658	0.91[AFR][1000 genomes]
rs45442295	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs45460091	0.91[AFR][1000 genomes]
rs45492098	0.92[EUR][1000 genomes]
rs45540134	0.92[EUR][1000 genomes]
rs45600842	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs45622743	0.92[EUR][1000 genomes]
rs4646440	0.95[AFR][1000 genomes]
rs4646447	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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];0.99[ASN][1000 genomes]
rs4646449	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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];0.99[ASN][1000 genomes]
rs4646450	0.80[CHB][hapmap];0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs4646453	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646456	1.00[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4646457	0.85[CHB][hapmap];0.81[CHD][hapmap];0.82[ASN][1000 genomes]
rs4646458	0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4646462	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4646465	0.81[ASN][1000 genomes]
rs58024720	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58222677	0.92[EUR][1000 genomes]
rs59172435	0.89[ASN][1000 genomes]
rs60298785	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs60301933	0.82[AMR][1000 genomes]
rs60865030	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61159815	0.92[EUR][1000 genomes]
rs61337492	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61402640	0.92[EUR][1000 genomes]
rs61543997	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61593387	0.89[ASN][1000 genomes]
rs6465750	0.85[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs72494451	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72494452	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72494453	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72494454	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72494456	0.89[ASN][1000 genomes]
rs72494458	0.89[AFR][1000 genomes]
rs776741	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776742	0.83[ASN][1000 genomes]
rs776744	0.83[ASN][1000 genomes]
rs776745	0.83[ASN][1000 genomes]
rs776746	0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs7798931	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7808022	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs8175345	1.00[ASW][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs8175346	0.82[EUR][1000 genomes]
rs939955	0.89[ASN][1000 genomes]
rs940336	0.92[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4646446	BUD31	cis	lymphoblastoid	seeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99235800-99276400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr7:99243000-99278800	Weak transcription	Brain Angular Gyrus	brain
3	chr7:99243600-99276800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr7:99251600-99276400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:99254400-99275400	Weak transcription	Fetal Stomach	stomach
6	chr7:99255800-99277000	Weak transcription	Fetal Brain Male	brain
7	chr7:99258400-99276400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr7:99258600-99276600	Weak transcription	Colon Smooth Muscle	Colon
9	chr7:99260200-99277000	Weak transcription	Spleen	Spleen
10	chr7:99260600-99276600	Weak transcription	Adipose Nuclei	Adipose
11	chr7:99260600-99276800	Weak transcription	Left Ventricle	heart
12	chr7:99261400-99277000	Weak transcription	Small Intestine	intestine
13	chr7:99263600-99277400	Weak transcription	Aorta	Aorta
14	chr7:99269000-99276600	Weak transcription	HMEC	breast
15	chr7:99272600-99275600	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr7:99273000-99276400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr7:99273000-99276800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr7:99273200-99276800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:99273400-99275400	Enhancers	HepG2	liver
20	chr7:99273400-99277000	Transcr. at gene 5' and 3'	Liver	Liver
21	chr7:99273600-99275600	Genic enhancers	Gastric	stomach
22	chr7:99273800-99275400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr7:99273800-99276000	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
24	chr7:99273800-99290400	Weak transcription	Primary T cells from cord blood	blood
25	chr7:99274000-99275200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr7:99274400-99275200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr7:99274400-99276200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
28	chr7:99274400-99276800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr7:99274600-99275200	Genic enhancers	Rectal Mucosa Donor 31	rectum
30	chr7:99274600-99275600	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
31	chr7:99274600-99275800	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
32	chr7:99274600-99276600	Enhancers	K562	blood
33	chr7:99274800-99275200	Enhancers	Pancreas	Pancrea
34	chr7:99274800-99275400	Enhancers	Lung	lung
35	chr7:99274800-99275800	Genic enhancers	Fetal Lung	lung
36	chr7:99275000-99275200	Enhancers	A549	lung
37	chr7:99275000-99275400	Weak transcription	Colonic Mucosa	Colon
38	chr7:99275000-99275400	Genic enhancers	Esophagus	oesophagus
39	chr7:99275000-99276400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr7:99275000-99276600	Weak transcription	NHDF-Ad	bronchial
41	chr7:99275000-99277600	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr7:99275000-99277600	Active TSS	Stomach Mucosa	stomach

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