Variant report

Variant	rs249003
Chromosome Location	chr5:79782632-79782633
allele	A/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	POLR2A	chr5:79782526-79782726	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr5:79782359-79782804	U87	brain:	n/a	n/a
3	POLR2A	chr5:79782311-79783030	SK-N-MC	brain:	n/a	n/a
4	FOXA1	chr5:79782324-79782669	T-47D	breast:	n/a	n/a
5	POLR2A	chr5:79782253-79782756	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr5:79782537-79782672	H1-hESC	embryonic stem cell:	n/a	n/a
7	FOXA1	chr5:79782371-79782763	T-47D	breast:	n/a	n/a
8	POLR2A	chr5:79782376-79783253	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:79781713..79786255-chr5:79948613..79954295,12	MCF-7	breast:
2	chr5:79775554..79779263-chr5:79781101..79783184,3	K562	blood:
3	chr5:79776960..79779263-chr5:79781101..79783184,2	K562	blood:

Variant related genes	Relation type
FAM151B	TF binding region
ENSG00000113318	Chromatin interaction
ENSG00000228716	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10433	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10474629	1.00[MEX][hapmap]
rs10942926	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1097307	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1097308	0.85[ASN][1000 genomes]
rs1097309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1102116	1.00[ASN][1000 genomes]
rs1103116	0.87[ASN][1000 genomes]
rs13354660	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1363775	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs168938	0.85[ASN][1000 genomes]
rs168939	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs168940	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs171595	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs171596	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171821	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs173597	1.00[ASN][1000 genomes]
rs173598	0.82[ASN][1000 genomes]
rs173599	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs174075	0.95[ASN][1000 genomes]
rs174076	1.00[CHB][hapmap];0.86[YRI][hapmap]
rs1820119	0.95[ASN][1000 genomes]
rs185100	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs187478	1.00[ASN][1000 genomes]
rs187479	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs192313	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs194540	0.83[ASN][1000 genomes]
rs2251759	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs248995	0.85[CHB][hapmap];1.00[CHD][hapmap]
rs248999	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs249000	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs249001	1.00[ASN][1000 genomes]
rs249004	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249005	1.00[ASN][1000 genomes]
rs249006	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249016	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs249020	0.83[ASN][1000 genomes]
rs249021	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs249023	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs249024	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs249025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs249026	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs249027	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs249028	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs249029	1.00[ASN][1000 genomes]
rs249030	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249031	1.00[ASN][1000 genomes]
rs249032	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs249033	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs249037	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs249038	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs249039	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2544591	1.00[CHB][hapmap]
rs2544592	0.85[ASN][1000 genomes]
rs2544593	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2544598	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2544599	0.95[ASN][1000 genomes]
rs2544600	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2544603	0.95[ASN][1000 genomes]
rs2544604	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2547487	0.85[ASN][1000 genomes]
rs259023	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.85[ASN][1000 genomes]
rs259024	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.85[ASN][1000 genomes]
rs259025	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs259026	0.85[ASN][1000 genomes]
rs259027	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[ASN][1000 genomes]
rs259028	1.00[ASW][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs259029	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259030	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs259031	0.95[ASN][1000 genomes]
rs259032	0.95[ASN][1000 genomes]
rs259033	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs259034	0.95[ASN][1000 genomes]
rs259037	1.00[CHB][hapmap]
rs259038	1.00[CHB][hapmap]
rs259039	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs259042	1.00[CHB][hapmap]
rs259043	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs259044	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs259045	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs259047	1.00[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs259048	1.00[CHB][hapmap]
rs259049	1.00[JPT][hapmap]
rs259051	0.80[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs259052	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs259053	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs259054	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs259055	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2599508	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3095851	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3096111	0.80[ASN][1000 genomes]
rs394076	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs394170	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs399261	1.00[ASN][1000 genomes]
rs401612	0.95[ASN][1000 genomes]
rs408899	1.00[ASN][1000 genomes]
rs4704674	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs557346	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6887302	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs701380	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs835726	0.82[ASN][1000 genomes]
rs835729	0.87[ASN][1000 genomes]
rs856765	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs856772	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs863163	1.00[ASN][1000 genomes]
rs969567	0.95[ASN][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	nsv948807	chr5:79549207-79805765	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1028027	chr5:79694699-79841752	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs249003	ZFYVE16	cis	lymphoblastoid	seeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79744800-79783200	Weak transcription	Colonic Mucosa	Colon
2	chr5:79759400-79782800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:79765600-79783400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:79766600-79783400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr5:79766800-79782800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:79767800-79783600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:79768200-79782800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:79768200-79783400	Weak transcription	HSMMtube	muscle
9	chr5:79768400-79783400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr5:79771000-79782800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr5:79771200-79783000	Weak transcription	NH-A	brain
12	chr5:79771400-79782800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr5:79771400-79783000	Weak transcription	Fetal Brain Male	brain
14	chr5:79771600-79783400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr5:79771600-79783400	Weak transcription	NHDF-Ad	bronchial
16	chr5:79772000-79782800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr5:79772000-79783200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:79772000-79783200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr5:79772000-79783400	Weak transcription	Left Ventricle	heart
20	chr5:79772000-79783400	Weak transcription	HUVEC	blood vessel
21	chr5:79772400-79783400	Weak transcription	Psoas Muscle	Psoas
22	chr5:79772400-79783400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr5:79775800-79782800	Weak transcription	HMEC	breast
24	chr5:79775800-79782800	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr5:79776000-79782800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:79776000-79783000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr5:79776600-79782800	Weak transcription	Stomach Mucosa	stomach
28	chr5:79777000-79782800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:79777200-79782800	Weak transcription	NHEK	skin
30	chr5:79777200-79783200	Weak transcription	HSMM	muscle
31	chr5:79777200-79783400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:79777400-79782800	Weak transcription	Colon Smooth Muscle	Colon
33	chr5:79777400-79783400	Weak transcription	Ovary	ovary
34	chr5:79777400-79783600	Weak transcription	Aorta	Aorta
35	chr5:79779600-79782800	Weak transcription	Liver	Liver
36	chr5:79779800-79782800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:79779800-79783000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr5:79779800-79783000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr5:79779800-79783200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:79779800-79783200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr5:79779800-79783400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:79779800-79783600	Weak transcription	Gastric	stomach
43	chr5:79780200-79782800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr5:79780200-79783000	Weak transcription	Fetal Thymus	thymus
45	chr5:79780200-79783200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr5:79780200-79783400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr5:79780400-79783000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr5:79780400-79783000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr5:79780400-79783000	Weak transcription	Fetal Muscle Leg	muscle
50	chr5:79780400-79783200	Weak transcription	Fetal Intestine Large	intestine

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