Variant report

Variant	rs61654248
Chromosome Location	chr3:56718030-56718031
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	GATA1	chr3:56716189-56718152	PBDE	blood:	n/a	chr3:56717810-56717821
2	E2F6	chr3:56716268-56718072	A549	lung:	n/a	chr3:56717409-56717419 chr3:56717410-56717418 chr3:56717098-56717107 chr3:56717408-56717419 chr3:56717562-56717571 chr3:56717410-56717418 chr3:56717307-56717316 chr3:56717411-56717418 chr3:56717410-56717418
3	TCF7L2	chr3:56717403-56718599	HEK293	kidney:	n/a	n/a
4	E2F6	chr3:56715929-56718143	H1-hESC	embryonic stem cell:	n/a	chr3:56717409-56717419 chr3:56717410-56717418 chr3:56717098-56717107 chr3:56717408-56717419 chr3:56717562-56717571 chr3:56717410-56717418 chr3:56717307-56717316 chr3:56717411-56717418 chr3:56717410-56717418
5	SETDB1	chr3:56717252-56718475	U2OS	brain:	n/a	n/a
6	ZNF263	chr3:56716001-56718555	HEK293-T-REx	kidney:	n/a	chr3:56717929-56717938 chr3:56717242-56717251
7	KAP1	chr3:56717363-56718703	HEK293	kidney:	n/a	chr3:56717806-56717814
8	KAP1	chr3:56717375-56718687	U2OS	brain:	n/a	chr3:56717806-56717814

No.	Distal block	Cell Line	Cell type
1	chr3:56705021..56708606-chr3:56714722..56718211,5	MCF-7	breast:
2	chr3:56589231..56591997-chr3:56715959..56718849,3	K562	blood:
3	chr3:56702147..56705420-chr3:56716741..56719178,3	MCF-7	breast:
4	chr3:56589586..56592975-chr3:56714350..56719200,6	K562	blood:
5	chr3:56715514..56718317-chr3:56833414..56836251,4	MCF-7	breast:

Variant related genes	Relation type
FAM208A	TF binding region
ENSG00000180376	Chromatin interaction
ENSG00000163946	Chromatin interaction
ENSG00000163947	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs11130522	0.85[EUR][1000 genomes]
rs1388252	0.85[EUR][1000 genomes]
rs1491162	0.85[EUR][1000 genomes]
rs1491167	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17216678	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17216712	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17216754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17288866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17288873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276469	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4292200	0.84[ASN][1000 genomes]
rs56758331	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57861120	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58457441	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59835031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59897254	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60606369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61456176	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61747994	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62249737	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62251182	0.92[EUR][1000 genomes]
rs62251183	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62251188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251192	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62251193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251228	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62251235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251239	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251240	0.89[EUR][1000 genomes]
rs62251241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62254329	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62255965	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62255966	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62255967	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62255969	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62255970	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62255971	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62255972	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62255973	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62255974	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62255977	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62255978	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62255980	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62255981	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256011	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256013	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62256014	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256017	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256018	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256019	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256020	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256022	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62256023	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782254	0.81[EUR][1000 genomes]
rs6788512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6810125	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73075746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73081816	0.92[EUR][1000 genomes]
rs73081836	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73081850	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73083715	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73083725	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638200	0.81[EUR][1000 genomes]
rs955247	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3327056	chr3:56715937-56718485	Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56717400-56718200	ZNF genes & repeats	Placenta	Placenta
2	chr3:56717400-56718200	ZNF genes & repeats	NHEK	skin
3	chr3:56717400-56718400	ZNF genes & repeats	HSMM	muscle
4	chr3:56717400-56718600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:56717600-56718400	Enhancers	HepG2	liver
6	chr3:56717600-56718600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:56717600-56718800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:56717600-56725200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:56717600-56725200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:56717800-56718200	Enhancers	Primary T cells fromperipheralblood	blood
11	chr3:56717800-56718200	ZNF genes & repeats	Colon Smooth Muscle	Colon
12	chr3:56717800-56718200	Weak transcription	NH-A	brain
13	chr3:56717800-56718600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:56717800-56718600	ZNF genes & repeats	GM12878-XiMat	blood
15	chr3:56717800-56718800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr3:56717800-56719400	Weak transcription	Fetal Kidney	kidney
17	chr3:56717800-56720200	Weak transcription	Fetal Lung	lung
18	chr3:56717800-56720800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:56717800-56722000	Weak transcription	Primary B cells from cord blood	blood
20	chr3:56717800-56725200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:56717800-56725200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:56717800-56726800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:56718000-56718200	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr3:56718000-56719000	Strong transcription	Fetal Thymus	thymus
25	chr3:56718000-56719400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:56718000-56719600	Weak transcription	Fetal Stomach	stomach
27	chr3:56718000-56719800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:56718000-56722000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr3:56718000-56722200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:56718000-56723400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:56718000-56725200	Weak transcription	Dnd41	blood
32	chr3:56718000-56725200	Weak transcription	HMEC	breast
33	chr3:56718000-56727000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr3:56718000-56727400	Weak transcription	HSMMtube	muscle

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