Variant report

Variant	rs3805363
Chromosome Location	chr17:46241622-46241623
allele	C/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	CTCF	chr17:46241189-46241657	HCT-116	colon:	n/a	chr17:46241362-46241380
2	RAD21	chr17:46241112-46241624	HCT-116	colon:	n/a	chr17:46241363-46241382

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46241394..46243371-chr17:46694152..46695794,2	K562	blood:
2	chr17:46240659..46244208-chr17:46251439..46255142,4	MCF-7	breast:

Variant related genes	Relation type
SKAP1	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1002330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10445339	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10445377	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10853098	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11079814	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11870056	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11872095	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12150533	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12452956	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12603115	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12603380	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12941830	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12947089	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12948810	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1316657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1377201	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1452666	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1452667	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17620033	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17681336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1860862	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1860863	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2021752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2021811	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2041572	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2060876	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs208005	0.81[ASN][1000 genomes]
rs208008	0.81[ASN][1000 genomes]
rs208009	0.81[ASN][1000 genomes]
rs208019	0.81[ASN][1000 genomes]
rs2109982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2123341	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2278868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305433	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2325784	0.80[ASN][1000 genomes]
rs2325804	0.81[ASN][1000 genomes]
rs2938483	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34949267	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3792692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3792694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3805370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3805371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3815472	0.81[ASN][1000 genomes]
rs3897986	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3944039	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4793779	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4794447	0.86[ASN][1000 genomes]
rs4794505	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4794517	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4794525	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55982346	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62066407	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62066447	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6504108	0.93[ASN][1000 genomes]
rs66683298	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67446770	0.86[EUR][1000 genomes]
rs7210149	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7213876	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7219967	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7220619	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7220768	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7220922	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7223867	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7225435	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7225550	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7225865	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7501770	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs758999	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8069064	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8069263	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8072282	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8075270	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8079616	0.81[ASN][1000 genomes]
rs882380	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs954226	0.85[EUR][1000 genomes];0.82[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	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 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	chr17:46216400-46251400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr17:46220800-46249000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr17:46230600-46245000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr17:46231000-46243800	Weak transcription	Primary B cells from cord blood	blood
5	chr17:46236000-46250200	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr17:46236200-46244200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr17:46236400-46242600	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr17:46236600-46242600	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr17:46236800-46244200	Strong transcription	Primary T cells from cord blood	blood
10	chr17:46237400-46242000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr17:46238200-46250800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr17:46238600-46246600	Weak transcription	Thymus	Thymus
13	chr17:46239200-46246400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr17:46239200-46253800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr17:46240000-46242200	Weak transcription	Pancreas	Pancrea
16	chr17:46240000-46246600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr17:46240000-46250400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr17:46240200-46244600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr17:46240200-46246400	Weak transcription	Fetal Thymus	thymus
20	chr17:46240200-46246800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr17:46241000-46241800	Enhancers	A549	lung
22	chr17:46241000-46242600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr17:46241000-46245000	Enhancers	GM12878-XiMat	blood
24	chr17:46241000-46250200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr17:46241000-46253200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr17:46241200-46241800	Enhancers	Liver	Liver
27	chr17:46241200-46242200	Weak transcription	Brain Germinal Matrix	brain
28	chr17:46241200-46242200	Weak transcription	Fetal Intestine Large	intestine
29	chr17:46241200-46244800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr17:46241200-46244800	Weak transcription	Fetal Intestine Small	intestine
31	chr17:46241200-46246000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr17:46241200-46247400	Weak transcription	Stomach Mucosa	stomach
33	chr17:46241400-46243200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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