Variant report

Variant	rs17002849
Chromosome Location	chr4:78873629-78873630
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:2819382..2822249-chr4:78873514..78875877,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167978	Chromatin interaction
ENSG00000265864	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10033527	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10033613	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1021824	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1021826	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12641050	0.84[ASN][1000 genomes]
rs13101418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13106067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13114091	0.84[ASN][1000 genomes]
rs2088994	0.82[ASN][1000 genomes]
rs2102191	0.81[ASN][1000 genomes]
rs28404443	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34459497	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34751953	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34850103	0.84[ASN][1000 genomes]
rs35648590	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35979107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4453957	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4571357	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4577601	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4859509	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4859511	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4859888	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4859889	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61207396	0.82[ASN][1000 genomes]
rs62302728	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62302732	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62310785	0.82[ASN][1000 genomes]
rs6533282	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6533291	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6533344	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6533345	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66825464	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6811736	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6814912	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6845998	0.84[ASN][1000 genomes]
rs6848029	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6854895	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7670157	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7676660	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7695874	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7698627	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7698629	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs905376	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752050	chr4:78693311-78975321	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1010714	chr4:78742505-78991030	Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv516836	chr4:78748977-78981919	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv594704	chr4:78748977-78981919	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv461562	chr4:78757015-78981919	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv461563	chr4:78757015-78981919	Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv594705	chr4:78757015-78981919	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1008217	chr4:78777531-78957311	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv537145	chr4:78777531-78957311	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers 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	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17002849	HMGB1P44	cis	Muscle Skeletal	GTEx
rs17002849	MRPL1	Cis_1M	lymphoblastoid	RTeQTL
rs17002849	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78785000-78874400	Weak transcription	Right Ventricle	heart
2	chr4:78806000-78881000	Weak transcription	Brain Hippocampus Middle	brain
3	chr4:78806600-78875600	Weak transcription	Colonic Mucosa	Colon
4	chr4:78809600-78881200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr4:78814600-78874400	Weak transcription	Pancreas	Pancrea
6	chr4:78816400-78876000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr4:78816600-78875800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:78830400-78877000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr4:78849400-78876600	Weak transcription	Colon Smooth Muscle	Colon
10	chr4:78849600-78881000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:78850200-78881000	Weak transcription	A549	lung
12	chr4:78852000-78881200	Weak transcription	Lung	lung
13	chr4:78852600-78878200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:78853000-78874200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:78853200-78874600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr4:78853200-78878000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:78853200-78880800	Weak transcription	Osteobl	bone
18	chr4:78853200-78881000	Weak transcription	Brain Anterior Caudate	brain
19	chr4:78853400-78873800	Weak transcription	NH-A	brain
20	chr4:78853400-78874600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:78853800-78876400	Weak transcription	Fetal Heart	heart
22	chr4:78853800-78877600	Weak transcription	NHEK	skin
23	chr4:78854000-78874400	Weak transcription	Fetal Intestine Large	intestine
24	chr4:78854200-78877800	Weak transcription	HSMMtube	muscle
25	chr4:78859400-78879000	Weak transcription	Small Intestine	intestine
26	chr4:78860000-78877800	Weak transcription	Esophagus	oesophagus
27	chr4:78860600-78877400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:78863400-78880800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr4:78864000-78876400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr4:78865000-78875600	Weak transcription	Fetal Brain Male	brain
31	chr4:78865600-78876600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:78865600-78877600	Weak transcription	Fetal Stomach	stomach
33	chr4:78865800-78875800	Weak transcription	HMEC	breast
34	chr4:78865800-78881000	Weak transcription	Psoas Muscle	Psoas
35	chr4:78866200-78875600	Weak transcription	Thymus	Thymus
36	chr4:78866600-78875000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:78866800-78877800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr4:78866800-78881000	Weak transcription	Fetal Kidney	kidney
39	chr4:78867000-78875800	Weak transcription	Fetal Muscle Leg	muscle
40	chr4:78867200-78877600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr4:78867600-78874600	Weak transcription	Primary T cells from cord blood	blood
42	chr4:78867600-78875800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr4:78867600-78876400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr4:78868600-78881000	Weak transcription	Brain Angular Gyrus	brain
45	chr4:78869000-78875600	Weak transcription	NHLF	lung
46	chr4:78869000-78879600	Weak transcription	Spleen	Spleen
47	chr4:78869200-78874400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr4:78869600-78877600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr4:78870200-78873800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr4:78870200-78876200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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