Variant report

Variant	rs3817163
Chromosome Location	chr2:54893237-54893238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:54892181-54896917	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:54892163-54894444	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:54889935-54893954	K562	blood:	n/a	n/a
4	POLR2A	chr2:54889669-54901118	HepG2	liver:	n/a	n/a
5	EP300	chr2:54893170-54893239	GM12878	blood:	n/a	n/a
6	NFIC	chr2:54893203-54894233	SK-N-SH	brain:	n/a	n/a
7	CTCF	chr2:54892218-54893698	A549	lung:	n/a	chr2:54892717-54892738 chr2:54892715-54892733 chr2:54892716-54892732
8	FOSL2	chr2:54893083-54894679	HepG2	liver:	n/a	chr2:54893631-54893641 chr2:54893633-54893640 chr2:54893632-54893641 chr2:54893630-54893642 chr2:54893631-54893640 chr2:54893631-54893641
9	POLR2A	chr2:54892497-54893268	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr2:54892273-54895690	A549	lung:	n/a	n/a
11	NFIC	chr2:54893090-54894274	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr2:54892162-54893784	GM12878	blood:	n/a	n/a
13	MBD4	chr2:54892477-54893452	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:54893211-54893261	HPAEpiC	pulmonary alveolar:	n/a
2	chr2:54893211-54893261	NB4	blood:	n/a
3	chr2:54893211-54893261	Caco-2	colon:	n/a
4	chr2:54893211-54893261	GM12891	blood:	n/a
5	chr2:54893211-54893261	K562	blood:	n/a
6	chr2:54893211-54893261	LNCaP	prostate:	n/a
7	chr2:54893211-54893261	HUVEC	blood vessel:	n/a
8	chr2:54893211-54893261	PANC-1	pancreas:	n/a
9	chr2:54893211-54893261	CMK	blood:	n/a
10	chr2:54893211-54893261	Jurkat	blood:	n/a
11	chr2:54893211-54893261	AG09319	gingival:	n/a
12	chr2:54893211-54893261	PrEC	prostate:	n/a
13	chr2:54893211-54893261	Hepatocyte	liver:	n/a
14	chr2:54893211-54893261	HCT-116	colon:	n/a
15	chr2:54893211-54893261	GM06990	blood:	n/a
16	chr2:54893211-54893261	HCPEpiC	choroid plexus:	n/a
17	chr2:54893211-54893261	BE2_C	brain:	n/a
18	chr2:54893211-54893261	HRPEpiC	eye:	n/a
19	chr2:54893211-54893261	AG10803	skin:	n/a
20	chr2:54893211-54893261	A549	lung:	n/a
21	chr2:54893211-54893261	PFSK-1	brain:	n/a
22	chr2:54893211-54893261	AG09309	skin:	n/a
23	chr2:54893211-54893261	AG04450	lung:	fetal
24	chr2:54893211-54893261	GM12878	blood:	n/a
25	chr2:54893211-54893261	NT2-D1	testis:	n/a
26	chr2:54893211-54893261	AoSMC	blood vessel:	n/a
27	chr2:54893211-54893261	HAEpiC	amniotic membrane:	n/a
28	chr2:54893211-54893261	SK-N-SH	brain:	n/a
29	chr2:54893211-54893261	HRE	kidney:	n/a
30	chr2:54893211-54893261	SK-N-SH_RA	brain:	n/a
31	chr2:54893211-54893261	Hela-S3	cervix:	n/a
32	chr2:54893211-54893261	SK-N-MC	brain:	n/a
33	chr2:54893211-54893261	HCM	heart:	n/a
34	chr2:54893211-54893261	MCF10A-Er-Src	breast:	n/a
35	chr2:54893211-54893261	HIPEpiC	eye:	n/a
36	chr2:54893211-54893261	H1-hESC	embryonic stem cell:	embryo
37	chr2:54893211-54893261	NH-A	brain:	n/a
38	chr2:54893211-54893261	BJ	skin:	n/a
39	chr2:54893211-54893261	HepG2	liver:	n/a
40	chr2:54893211-54893261	U87	brain:	n/a
41	chr2:54893211-54893261	HMEC	breast:	n/a
42	chr2:54893211-54893261	NHDF-neo	bronchial:	n/a
43	chr2:54893211-54893261	IMR90	lung:	fetal
44	chr2:54893211-54893261	HEEpiC	esophagus:	n/a
45	chr2:54893211-54893261	SAEC	small airway:	n/a
46	chr2:54893211-54893261	ProgFib	skin:	n/a
47	chr2:54893211-54893261	GM12892	blood:	n/a
48	chr2:54893211-54893261	MCF-7	breast:	n/a
49	chr2:54893211-54893261	RPTEC	kidney:	n/a
50	chr2:54893211-54893261	ECC-1	luminal epithelium:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54891251..54894116-chr2:54898637..54900968,3	MCF-7	breast:
2	chr2:54891342..54894033-chr2:54900112..54903106,2	K562	blood:
3	chr2:54892654..54893275-chr2:54931608..54932460,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000238018	TF binding region
ENSG00000238018	CpG island

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10164713	0.91[EUR][1000 genomes]
rs1027950	0.90[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs1052788	0.87[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs1052820	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1112919	0.86[GIH][hapmap];0.88[TSI][hapmap]
rs12467653	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12473338	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12475342	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12475598	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12615589	0.94[EUR][1000 genomes]
rs12620195	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1510612	0.83[AMR][1000 genomes]
rs17046153	0.85[AMR][1000 genomes]
rs17416284	1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2007020	0.85[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap]
rs3796012	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4283459	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4519565	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs4557016	0.91[EUR][1000 genomes]
rs4567979	0.85[EUR][1000 genomes]
rs4671223	0.88[CEU][hapmap]
rs4671224	0.88[CEU][hapmap];0.84[GIH][hapmap];0.90[TSI][hapmap]
rs4671227	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4671229	0.90[CEU][hapmap]
rs4671952	0.92[CEU][hapmap];0.82[GIH][hapmap]
rs4671959	0.95[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs4671962	0.96[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs4671964	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4671965	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671966	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4671968	0.85[AMR][1000 genomes]
rs59871921	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60294349	0.86[EUR][1000 genomes]
rs6545428	0.92[CEU][hapmap]
rs6545433	0.89[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6705756	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6738725	1.00[ASW][hapmap];0.91[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.80[JPT][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs6739099	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67457439	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72618663	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs72618664	0.83[EUR][1000 genomes]
rs72618665	0.85[AMR][1000 genomes]
rs72618667	0.83[AMR][1000 genomes]
rs9309255	0.92[CEU][hapmap];0.84[GIH][hapmap];0.90[TSI][hapmap]

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	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3817163	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL
rs3817163	EML6	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54838800-54893400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:54839400-54895000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:54841200-54897800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:54846400-54895600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:54846400-54896600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:54846600-54898000	Strong transcription	Dnd41	blood
7	chr2:54846800-54895400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:54861800-54898600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:54862200-54896600	Strong transcription	Primary hematopoietic stem cells	blood
10	chr2:54862600-54893400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:54862600-54898400	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr2:54863000-54895000	Strong transcription	Duodenum Mucosa	Duodenum
13	chr2:54863000-54898600	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr2:54863000-54899400	Strong transcription	Primary T cells from cord blood	blood
15	chr2:54863600-54897000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
16	chr2:54863800-54897400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:54863800-54898600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr2:54864200-54893600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr2:54865400-54898400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:54865800-54898200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:54866400-54897200	Strong transcription	Primary B cells from cord blood	blood
22	chr2:54867200-54897800	Strong transcription	Primary B cells from peripheral blood	blood
23	chr2:54867200-54898200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr2:54868800-54898600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:54869000-54896400	Strong transcription	Colonic Mucosa	Colon
26	chr2:54869600-54893400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:54869600-54898600	Strong transcription	Fetal Thymus	thymus
28	chr2:54869800-54895200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:54869800-54897600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:54878400-54897000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr2:54879600-54898400	Strong transcription	GM12878-XiMat	blood
32	chr2:54880200-54898400	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr2:54880200-54898400	Strong transcription	Thymus	Thymus
34	chr2:54882400-54894800	Weak transcription	K562	blood
35	chr2:54883000-54895000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:54883000-54899400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr2:54885000-54896400	Strong transcription	Hela-S3	cervix
38	chr2:54886800-54896600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:54889000-54893600	Genic enhancers	HepG2	liver
40	chr2:54889200-54898600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:54890000-54896400	Genic enhancers	Liver	Liver
42	chr2:54890800-54895600	Genic enhancers	Left Ventricle	heart
43	chr2:54890800-54898200	Genic enhancers	Brain Inferior Temporal Lobe	brain
44	chr2:54891000-54899400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:54891200-54899800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr2:54891400-54895400	Genic enhancers	Fetal Muscle Leg	muscle
47	chr2:54891400-54895600	Genic enhancers	Lung	lung
48	chr2:54891400-54896000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:54891400-54896600	Genic enhancers	Placenta	Placenta
50	chr2:54891600-54893800	Genic enhancers	A549	lung

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