Variant report

Variant	rs55828309
Chromosome Location	chr3:156884667-156884668
allele	C/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	PAX5	chr3:156884368-156884672	GM12891	blood:	n/a	chr3:156884476-156884485
2	BHLHE40	chr3:156884432-156884707	GM12878	blood:	n/a	n/a
3	BATF	chr3:156884356-156884764	GM12878	blood:	n/a	chr3:156884588-156884597
4	TBP	chr3:156884466-156884692	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156529223..156530794-chr3:156884048..156887029,2	MCF-7	breast:

Variant related genes	Relation type
KRT18P34	TF binding region

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10936061	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936062	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936063	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936064	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936065	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936066	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936067	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10936068	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10936069	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10936074	0.93[EUR][1000 genomes]
rs10936075	0.82[EUR][1000 genomes]
rs1157738	0.80[AMR][1000 genomes]
rs12488480	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489453	0.94[EUR][1000 genomes]
rs12489799	0.96[EUR][1000 genomes]
rs12490836	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12492801	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12496051	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12496111	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12497891	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12630209	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12633429	0.82[EUR][1000 genomes]
rs12634818	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12635088	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636125	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16827318	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16827322	0.80[AMR][1000 genomes]
rs16827352	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17552941	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995304	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2321740	0.88[EUR][1000 genomes]
rs35910014	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3935750	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41272613	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4371471	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4383467	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4413278	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4608646	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679788	0.94[EUR][1000 genomes]
rs4680340	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680343	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680345	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680347	0.80[AMR][1000 genomes]
rs4680349	0.85[EUR][1000 genomes]
rs5003893	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55835412	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55949516	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55953639	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56078410	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56263456	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57322659	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57511361	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59210914	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59279023	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59485606	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59865540	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60153077	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61149035	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62274129	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62274155	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62274156	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62274159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276460	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276461	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276462	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276465	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62276470	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62276471	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62276474	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276475	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276479	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62276480	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276488	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62276489	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62276490	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62276491	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62276495	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62276496	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62276497	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62276501	0.96[EUR][1000 genomes]
rs62276502	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62276504	0.94[EUR][1000 genomes]
rs62276505	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6441115	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441116	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441119	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768052	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6768074	0.93[EUR][1000 genomes]
rs6777922	0.87[AFR][1000 genomes]
rs6780205	0.93[EUR][1000 genomes]
rs6781682	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792479	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6805989	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806232	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6809307	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73154633	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73154649	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73154657	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73154659	0.94[EUR][1000 genomes]
rs73154671	0.86[EUR][1000 genomes]
rs73154682	0.84[EUR][1000 genomes]
rs73873800	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7610214	0.82[EUR][1000 genomes]
rs7621912	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626589	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7633004	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648599	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7652298	0.84[EUR][1000 genomes]
rs8180056	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8180057	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8925	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs949854	0.82[EUR][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	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv520331	chr3:156858300-156915650	Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156879000-156885600	Weak transcription	Psoas Muscle	Psoas
2	chr3:156879000-156891800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:156879000-156892000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:156879200-156891800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:156879200-156891800	Weak transcription	Fetal Stomach	stomach
6	chr3:156879200-156891800	Weak transcription	Fetal Thymus	thymus
7	chr3:156879200-156892000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:156879400-156891200	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:156879800-156891800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr3:156880000-156888800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:156880000-156891400	Weak transcription	Placenta	Placenta
12	chr3:156880000-156891400	Weak transcription	GM12878-XiMat	blood
13	chr3:156880200-156888400	Weak transcription	Primary B cells from cord blood	blood
14	chr3:156880200-156891600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:156880200-156891800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:156880400-156891600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:156881000-156891600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:156881200-156892200	Weak transcription	Small Intestine	intestine
19	chr3:156881800-156888400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:156881800-156892000	Weak transcription	Lung	lung
21	chr3:156882800-156884800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr3:156883000-156885800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:156883600-156886200	Enhancers	Liver	Liver
24	chr3:156883800-156885000	Enhancers	HepG2	liver
25	chr3:156883800-156886200	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr3:156884000-156886000	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr3:156884000-156886600	Enhancers	Fetal Intestine Small	intestine
28	chr3:156884000-156886800	Enhancers	Fetal Intestine Large	intestine
29	chr3:156884200-156885600	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr3:156884400-156885000	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr3:156884400-156885200	Enhancers	Fetal Kidney	kidney
32	chr3:156884600-156884800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:156884600-156885000	Weak transcription	Duodenum Mucosa	Duodenum

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