Variant report

Variant	rs41271878
Chromosome Location	chr6:56493073-56493074
allele	C/G/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	CEBPB	chr6:56493002-56493347	IMR90	lung:	n/a	chr6:56493165-56493178 chr6:56493167-56493176 chr6:56493165-56493178 chr6:56493165-56493176
2	CEBPB	chr6:56493000-56493263	MCF-7	breast:	n/a	chr6:56493165-56493178 chr6:56493167-56493176 chr6:56493165-56493178 chr6:56493165-56493176
3	GATA3	chr6:56492899-56493243	T-47D	breast:	n/a	n/a
4	POLR2A	chr6:56493059-56495607	MCF10A-Er-Src	breast:	n/a	n/a
5	GATA3	chr6:56492883-56493186	T-47D	breast:	n/a	n/a
6	POLR2A	chr6:56493035-56493160	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
DST	TF binding region

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1024196	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10484859	0.89[ASN][1000 genomes]
rs11961141	0.89[ASN][1000 genomes]
rs11963288	0.94[EUR][1000 genomes]
rs11966986	1.00[EUR][1000 genomes]
rs11967796	1.00[EUR][1000 genomes]
rs11968575	0.89[ASN][1000 genomes]
rs11970410	1.00[EUR][1000 genomes]
rs13192478	0.89[ASN][1000 genomes]
rs13192567	0.89[ASN][1000 genomes]
rs13210876	0.89[ASN][1000 genomes]
rs13213878	0.89[ASN][1000 genomes]
rs13219546	0.89[ASN][1000 genomes]
rs1407831	0.89[EUR][1000 genomes]
rs1535609	0.94[EUR][1000 genomes]
rs1535611	0.94[EUR][1000 genomes]
rs16887928	0.89[EUR][1000 genomes]
rs16888053	0.89[ASN][1000 genomes]
rs16888061	0.89[ASN][1000 genomes]
rs16888070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888106	1.00[EUR][1000 genomes]
rs16888135	0.89[ASN][1000 genomes]
rs2144407	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2180148	1.00[EUR][1000 genomes]
rs2207678	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2230863	0.89[ASN][1000 genomes]
rs2397224	0.89[EUR][1000 genomes]
rs28633631	1.00[EUR][1000 genomes]
rs2967960	0.89[ASN][1000 genomes]
rs3002003	0.89[ASN][1000 genomes]
rs3002004	0.89[ASN][1000 genomes]
rs34812826	0.89[ASN][1000 genomes]
rs34824960	0.89[ASN][1000 genomes]
rs35089136	0.89[ASN][1000 genomes]
rs35920751	0.89[ASN][1000 genomes]
rs3800026	0.94[EUR][1000 genomes]
rs3924307	0.94[EUR][1000 genomes]
rs41267673	1.00[EUR][1000 genomes]
rs41271848	0.89[EUR][1000 genomes]
rs41271850	0.89[EUR][1000 genomes]
rs41271854	0.94[EUR][1000 genomes]
rs41271856	0.94[EUR][1000 genomes]
rs41271872	1.00[EUR][1000 genomes]
rs41271876	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4256439	0.94[EUR][1000 genomes]
rs4275049	0.89[ASN][1000 genomes]
rs4288197	0.84[EUR][1000 genomes]
rs45442999	0.94[EUR][1000 genomes]
rs45553042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45564536	0.89[ASN][1000 genomes]
rs4574644	0.89[ASN][1000 genomes]
rs4640889	0.89[ASN][1000 genomes]
rs56094263	0.89[ASN][1000 genomes]
rs56991168	0.81[EUR][1000 genomes]
rs57289287	1.00[EUR][1000 genomes]
rs57350484	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57790896	1.00[EUR][1000 genomes]
rs57822928	0.94[EUR][1000 genomes]
rs58487319	0.81[EUR][1000 genomes]
rs58565063	1.00[EUR][1000 genomes]
rs58730144	0.94[EUR][1000 genomes]
rs59085778	0.89[ASN][1000 genomes]
rs59162324	0.89[ASN][1000 genomes]
rs59247267	0.89[ASN][1000 genomes]
rs59772940	1.00[EUR][1000 genomes]
rs59864125	0.94[EUR][1000 genomes]
rs60498201	0.89[ASN][1000 genomes]
rs62621210	0.94[EUR][1000 genomes]
rs6459165	0.89[ASN][1000 genomes]
rs6459167	1.00[EUR][1000 genomes]
rs6459168	1.00[EUR][1000 genomes]
rs6900572	1.00[EUR][1000 genomes]
rs6903517	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6903815	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6926134	0.89[ASN][1000 genomes]
rs6941626	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73455767	0.94[EUR][1000 genomes]
rs73455782	0.94[EUR][1000 genomes]
rs73455797	0.81[EUR][1000 genomes]
rs73465854	0.94[EUR][1000 genomes]
rs73746926	1.00[EUR][1000 genomes]
rs73746929	1.00[EUR][1000 genomes]
rs73747826	0.89[EUR][1000 genomes]
rs73747832	0.89[EUR][1000 genomes]
rs73749935	0.94[EUR][1000 genomes]
rs73749942	0.94[EUR][1000 genomes]
rs73749948	0.94[EUR][1000 genomes]
rs73749949	0.94[EUR][1000 genomes]
rs7749100	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7759479	1.00[EUR][1000 genomes]
rs7760503	1.00[EUR][1000 genomes]
rs7760515	1.00[EUR][1000 genomes]
rs7760542	1.00[EUR][1000 genomes]
rs7760701	1.00[EUR][1000 genomes]
rs7761027	1.00[EUR][1000 genomes]
rs7769014	0.94[EUR][1000 genomes]
rs7775134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS 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	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56408200-56496000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:56417000-56516400	Weak transcription	Pancreas	Pancrea
3	chr6:56432800-56513600	Weak transcription	Small Intestine	intestine
4	chr6:56441000-56524800	Weak transcription	Colonic Mucosa	Colon
5	chr6:56451800-56514200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:56452200-56514600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:56453000-56502200	Strong transcription	Muscle Satellite Cultured Cells	--
8	chr6:56453000-56506800	Strong transcription	HSMM	muscle
9	chr6:56457200-56501200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:56459000-56496200	Weak transcription	Fetal Kidney	kidney
11	chr6:56459000-56502400	Strong transcription	Osteobl	bone
12	chr6:56459000-56521000	Weak transcription	Spleen	Spleen
13	chr6:56460600-56496000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr6:56460600-56513600	Weak transcription	Stomach Mucosa	stomach
15	chr6:56470600-56502200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:56470800-56502600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:56474200-56501200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:56478000-56502600	Strong transcription	NHDF-Ad	bronchial
19	chr6:56478200-56501600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:56478400-56514600	Weak transcription	Lung	lung
21	chr6:56478600-56501800	Strong transcription	Adipose Nuclei	Adipose
22	chr6:56479400-56502600	Strong transcription	HMEC	breast
23	chr6:56479600-56495200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:56479800-56497400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:56480000-56501800	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:56480400-56493200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:56480600-56494200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr6:56480600-56495400	Strong transcription	NHEK	skin
29	chr6:56480600-56514600	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr6:56480800-56536400	Weak transcription	Gastric	stomach
31	chr6:56481000-56501600	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr6:56482000-56518200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:56482200-56501600	Strong transcription	Brain Anterior Caudate	brain
34	chr6:56482200-56505000	Weak transcription	Esophagus	oesophagus
35	chr6:56483400-56496000	Weak transcription	Right Ventricle	heart
36	chr6:56483400-56512600	Weak transcription	Psoas Muscle	Psoas
37	chr6:56485000-56514400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr6:56485600-56498200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:56485600-56507400	Weak transcription	Aorta	Aorta
40	chr6:56485800-56512400	Weak transcription	Fetal Stomach	stomach
41	chr6:56486000-56500200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr6:56486800-56493600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:56487000-56493400	Strong transcription	HUVEC	blood vessel
44	chr6:56487200-56501800	Strong transcription	Fetal Lung	lung
45	chr6:56487200-56502000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr6:56487600-56501000	Strong transcription	GM12878-XiMat	blood
47	chr6:56487600-56501800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr6:56487800-56494000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:56488000-56500800	Strong transcription	NH-A	brain
50	chr6:56488200-56493200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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