Variant report

Variant	rs28668361
Chromosome Location	chr5:74898137-74898138
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	RCOR1	chr5:74897396-74898515	IMR90	lung:	n/a	n/a
2	POLR2A	chr5:74897839-74898171	GM12892	blood:	n/a	n/a
3	RAD21	chr5:74897620-74898335	IMR90	lung:	n/a	n/a
4	POLR2A	chr5:74897791-74898255	GM12878	blood:	n/a	n/a
5	POLR2A	chr5:74897295-74898582	K562	blood:	n/a	n/a
6	POLR2A	chr5:74898029-74899595	IMR90	lung:	n/a	n/a
7	MAX	chr5:74897837-74898356	MCF-7	breast:	n/a	n/a
8	CEBPB	chr5:74897785-74898272	IMR90	lung:	n/a	n/a
9	STAT3	chr5:74897972-74898226	MCF10A-Er-Src	breast:	n/a	n/a
10	MAFK	chr5:74897868-74898336	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000248881	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10036682	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10038945	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10041470	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10055011	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10059022	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10061689	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10067900	0.89[EUR][1000 genomes]
rs10074747	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10076819	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10077427	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10078671	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474437	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12173076	0.85[EUR][1000 genomes]
rs13360099	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13361353	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1469051	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1553234	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1820049	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1909719	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2287710	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs253410	0.85[ASN][1000 genomes]
rs28408106	0.89[EUR][1000 genomes]
rs28612248	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28874007	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34339	0.85[ASN][1000 genomes]
rs34342	0.85[ASN][1000 genomes]
rs34343	0.85[ASN][1000 genomes]
rs34349	0.80[ASN][1000 genomes]
rs3804231	0.89[EUR][1000 genomes]
rs4703675	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704213	0.89[EUR][1000 genomes]
rs4704229	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56859362	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5744544	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5744545	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5744636	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5744667	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5744704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5744709	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5744712	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57907925	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58841453	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891560	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72633965	0.89[EUR][1000 genomes]
rs72633966	0.82[EUR][1000 genomes]
rs72633967	0.91[EUR][1000 genomes]
rs72633968	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72633969	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72633970	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72633971	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72633972	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72633973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72633974	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72633975	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633977	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7356633	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7726478	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs904743	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9293652	0.89[EUR][1000 genomes]
rs9293654	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9293655	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs979182	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882193	chr5:74656175-74917862	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv882196	chr5:74678937-74917862	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv882199	chr5:74757758-74946455	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv882202	chr5:74808417-74946455	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	esv1850196	chr5:74890618-75138443	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74833400-74906800	Weak transcription	Brain Substantia Nigra	brain
2	chr5:74841200-74899400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:74862800-74907200	Weak transcription	Esophagus	oesophagus
4	chr5:74863600-74905800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:74863800-74906800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:74864000-74899600	Weak transcription	Hela-S3	cervix
7	chr5:74864000-74907000	Weak transcription	Psoas Muscle	Psoas
8	chr5:74865800-74906800	Weak transcription	Colonic Mucosa	Colon
9	chr5:74867600-74907200	Weak transcription	Small Intestine	intestine
10	chr5:74871800-74900600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr5:74872400-74898400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr5:74873600-74907000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr5:74873800-74899200	Weak transcription	K562	blood
14	chr5:74873800-74901000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:74875200-74907000	Weak transcription	Right Ventricle	heart
16	chr5:74875800-74903400	Weak transcription	Fetal Thymus	thymus
17	chr5:74877000-74898400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:74877400-74899200	Weak transcription	HUVEC	blood vessel
19	chr5:74878200-74899000	Weak transcription	HMEC	breast
20	chr5:74878400-74898200	Weak transcription	Fetal Brain Male	brain
21	chr5:74878600-74901200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr5:74879000-74907000	Weak transcription	HepG2	liver
23	chr5:74884600-74901200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr5:74885400-74901000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:74889800-74906200	Weak transcription	Fetal Intestine Small	intestine
26	chr5:74889800-74906800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr5:74889800-74907200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr5:74890400-74907000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr5:74892800-74901000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:74892800-74907000	Weak transcription	Colon Smooth Muscle	Colon
31	chr5:74893000-74898800	Weak transcription	Fetal Kidney	kidney
32	chr5:74893200-74906800	Weak transcription	Stomach Mucosa	stomach
33	chr5:74893400-74901400	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr5:74894400-74908200	Weak transcription	GM12878-XiMat	blood
35	chr5:74894800-74899600	Strong transcription	Primary B cells from cord blood	blood
36	chr5:74895000-74898600	Weak transcription	Fetal Heart	heart
37	chr5:74895200-74899600	Strong transcription	HSMM	muscle
38	chr5:74895800-74900800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr5:74896200-74898400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:74896600-74900000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr5:74896600-74902000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr5:74896600-74907000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr5:74896600-74907000	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr5:74896600-74907000	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr5:74896600-74907200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr5:74896800-74898200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:74896800-74898400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr5:74896800-74900200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr5:74896800-74907000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:74897000-74898200	Strong transcription	Fetal Lung	lung

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