Variant report

Variant	rs249004
Chromosome Location	chr5:79782940-79782941
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	POLR2A	chr5:79782311-79783030	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr5:79782376-79783253	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:79782822..79786705-chr5:79948261..79952248,11	MCF-7	breast:
2	chr5:79781713..79786255-chr5:79948613..79954295,12	MCF-7	breast:
3	chr5:79775554..79779263-chr5:79781101..79783184,3	K562	blood:
4	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: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10433	1.00[ASN][1000 genomes]
rs10474621	0.92[EUR][1000 genomes]
rs10942926	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1097307	0.85[ASN][1000 genomes]
rs1097308	0.85[ASN][1000 genomes]
rs1097309	0.85[ASN][1000 genomes]
rs1102116	1.00[ASN][1000 genomes]
rs1103116	0.87[ASN][1000 genomes]
rs1104243	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13354660	0.92[EUR][1000 genomes]
rs13359253	0.92[EUR][1000 genomes]
rs1363775	0.95[ASN][1000 genomes]
rs1423113	0.92[EUR][1000 genomes]
rs16877755	0.92[EUR][1000 genomes]
rs16877757	0.92[EUR][1000 genomes]
rs168938	0.85[ASN][1000 genomes]
rs168939	0.95[ASN][1000 genomes]
rs168940	0.88[EUR][1000 genomes]
rs171595	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173597	1.00[ASN][1000 genomes]
rs173598	0.94[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs173599	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs174075	0.95[ASN][1000 genomes]
rs174076	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1820119	0.95[ASN][1000 genomes]
rs185100	0.92[ASN][1000 genomes]
rs187478	1.00[ASN][1000 genomes]
rs187479	1.00[ASN][1000 genomes]
rs192313	0.87[ASN][1000 genomes]
rs194540	0.83[ASN][1000 genomes]
rs194541	0.92[EUR][1000 genomes]
rs2251759	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs248999	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249000	0.88[ASN][1000 genomes]
rs249001	1.00[ASN][1000 genomes]
rs249003	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249005	1.00[ASN][1000 genomes]
rs249006	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249016	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs249020	0.83[ASN][1000 genomes]
rs249021	0.92[ASN][1000 genomes]
rs249023	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249024	0.95[ASN][1000 genomes]
rs249025	0.95[ASN][1000 genomes]
rs249026	0.95[ASN][1000 genomes]
rs249027	0.95[ASN][1000 genomes]
rs249028	0.95[ASN][1000 genomes]
rs249029	1.00[ASN][1000 genomes]
rs249030	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249031	1.00[ASN][1000 genomes]
rs249032	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249037	1.00[ASN][1000 genomes]
rs249038	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249039	0.95[ASN][1000 genomes]
rs2544591	0.92[EUR][1000 genomes]
rs2544592	0.85[ASN][1000 genomes]
rs2544593	0.85[ASN][1000 genomes]
rs2544598	0.95[ASN][1000 genomes]
rs2544599	0.95[ASN][1000 genomes]
rs2544600	0.95[ASN][1000 genomes]
rs2544603	0.95[ASN][1000 genomes]
rs2544604	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2547487	0.85[ASN][1000 genomes]
rs259023	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs259024	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs259025	0.85[ASN][1000 genomes]
rs259026	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs259027	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs259028	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259029	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs259030	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259031	0.95[ASN][1000 genomes]
rs259032	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259033	0.95[ASN][1000 genomes]
rs259034	0.95[ASN][1000 genomes]
rs259036	0.92[EUR][1000 genomes]
rs259037	0.92[EUR][1000 genomes]
rs259038	0.92[EUR][1000 genomes]
rs259040	0.92[EUR][1000 genomes]
rs259042	0.92[EUR][1000 genomes]
rs259044	0.87[EUR][1000 genomes]
rs259045	0.92[EUR][1000 genomes]
rs259046	0.92[EUR][1000 genomes]
rs259047	0.92[EUR][1000 genomes]
rs259048	0.88[EUR][1000 genomes]
rs259051	0.92[EUR][1000 genomes]
rs259052	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs259053	0.92[EUR][1000 genomes]
rs259054	0.92[EUR][1000 genomes]
rs259055	0.85[ASN][1000 genomes]
rs2599508	1.00[ASN][1000 genomes]
rs28496723	0.92[EUR][1000 genomes]
rs28555465	0.92[EUR][1000 genomes]
rs3095851	0.95[ASN][1000 genomes]
rs3096109	0.82[AFR][1000 genomes]
rs3096111	0.80[ASN][1000 genomes]
rs394076	1.00[ASN][1000 genomes]
rs394170	1.00[ASN][1000 genomes]
rs399261	1.00[ASN][1000 genomes]
rs401612	0.95[ASN][1000 genomes]
rs408899	1.00[ASN][1000 genomes]
rs4704674	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs557346	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6869519	0.92[EUR][1000 genomes]
rs6885891	0.90[EUR][1000 genomes]
rs6887302	0.90[EUR][1000 genomes]
rs701380	1.00[ASN][1000 genomes]
rs835726	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs835729	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs856765	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs856772	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[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

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79744800-79783200	Weak transcription	Colonic Mucosa	Colon
2	chr5:79765600-79783400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:79766600-79783400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:79767800-79783600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:79768200-79783400	Weak transcription	HSMMtube	muscle
6	chr5:79768400-79783400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:79771200-79783000	Weak transcription	NH-A	brain
8	chr5:79771400-79783000	Weak transcription	Fetal Brain Male	brain
9	chr5:79771600-79783400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:79771600-79783400	Weak transcription	NHDF-Ad	bronchial
11	chr5:79772000-79783200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr5:79772000-79783200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr5:79772000-79783400	Weak transcription	Left Ventricle	heart
14	chr5:79772000-79783400	Weak transcription	HUVEC	blood vessel
15	chr5:79772400-79783400	Weak transcription	Psoas Muscle	Psoas
16	chr5:79772400-79783400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr5:79776000-79783000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:79777200-79783200	Weak transcription	HSMM	muscle
19	chr5:79777200-79783400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:79777400-79783400	Weak transcription	Ovary	ovary
21	chr5:79777400-79783600	Weak transcription	Aorta	Aorta
22	chr5:79779800-79783000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr5:79779800-79783000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr5:79779800-79783200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:79779800-79783200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr5:79779800-79783400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:79779800-79783600	Weak transcription	Gastric	stomach
28	chr5:79780200-79783000	Weak transcription	Fetal Thymus	thymus
29	chr5:79780200-79783200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:79780200-79783400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:79780400-79783000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:79780400-79783000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr5:79780400-79783000	Weak transcription	Fetal Muscle Leg	muscle
34	chr5:79780400-79783200	Weak transcription	Fetal Intestine Large	intestine
35	chr5:79780600-79783000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:79780800-79783000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:79780800-79783200	Weak transcription	Fetal Intestine Small	intestine
38	chr5:79781000-79783200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr5:79781000-79783200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:79781000-79783400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr5:79781200-79783000	Weak transcription	Fetal Stomach	stomach
42	chr5:79781200-79783000	Weak transcription	A549	lung
43	chr5:79781200-79783200	Weak transcription	Pancreas	Pancrea
44	chr5:79781400-79783400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr5:79782200-79783200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr5:79782200-79785000	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr5:79782400-79783000	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr5:79782400-79783000	Enhancers	HepG2	liver
49	chr5:79782400-79783200	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr5:79782400-79783200	Enhancers	Primary T helper naive cells from peripheral blood	blood

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