Variant report

Variant	rs35459290
Chromosome Location	chr10:26986322-26986323
allele	CT/GC
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	MAX	chr10:26985900-26987411	HCT-116	colon:	n/a	chr10:26986852-26986863 chr10:26986851-26986866
2	TAF7	chr10:26985994-26986567	H1-hESC	embryonic stem cell:	n/a	n/a
3	BHLHE40	chr10:26985922-26987049	HepG2	liver:	n/a	chr10:26986481-26986497
4	GABPA	chr10:26985595-26987357	A549	lung:	n/a	n/a
5	POLR2A	chr10:26985958-26987069	K562	blood:	n/a	n/a
6	POLR2A	chr10:26985626-26987072	GM12892	blood:	n/a	n/a
7	POLR2A	chr10:26985686-26987003	HCT-116	colon:	n/a	n/a
8	POLR2A	chr10:26986285-26986537	H1-hESC	embryonic stem cell:	n/a	n/a
9	RELA	chr10:26985862-26986833	GM18951	blood:	n/a	n/a
10	MAX	chr10:26985963-26987200	SK-N-SH	brain:	n/a	chr10:26986852-26986863 chr10:26986851-26986866
11	REST	chr10:26985690-26987322	H1-neurons	neurons:	n/a	chr10:26986429-26986439 chr10:26987192-26987212
12	POLR2A	chr10:26985739-26986898	U87	brain:	n/a	n/a
13	NR2C2	chr10:26986170-26987023	HepG2	liver:	n/a	chr10:26986797-26986810
14	HEY1	chr10:26985912-26986951	K562	blood:	n/a	chr10:26986780-26986795 chr10:26986610-26986625 chr10:26986604-26986619
15	MAX	chr10:26985818-26987588	A549	lung:	n/a	chr10:26986852-26986863 chr10:26986851-26986866
16	GABPA	chr10:26985491-26987207	MCF-7	breast:	n/a	n/a
17	ELF1	chr10:26985948-26987082	MCF-7	breast:	n/a	chr10:26986333-26986342 chr10:26986153-26986162
18	CEBPB	chr10:26985841-26986411	K562	blood:	n/a	chr10:26986086-26986099 chr10:26986010-26986021 chr10:26985938-26985949
19	SIN3AK20	chr10:26986253-26986486	PANC-1	pancreas:	n/a	n/a
20	YY1	chr10:26986083-26986892	ECC-1	luminal epithelium:	n/a	chr10:26986410-26986421 chr10:26986611-26986622
21	TAF1	chr10:26985957-26986980	H1-hESC	embryonic stem cell:	n/a	n/a
22	CBX3	chr10:26985862-26986661	K562	blood:	n/a	n/a
23	RCOR1	chr10:26986021-26986435	K562	blood:	n/a	n/a
24	POLR2A	chr10:26986179-26987023	HepG2	liver:	n/a	n/a
25	GABPA	chr10:26985842-26987140	SK-N-SH	brain:	n/a	n/a
26	MAX	chr10:26985841-26987229	MCF-7	breast:	n/a	chr10:26986852-26986863 chr10:26986851-26986866
27	MAX	chr10:26985864-26987533	K562	blood:	n/a	chr10:26986852-26986863 chr10:26986851-26986866
28	YY1	chr10:26986036-26986954	GM12891	blood:	n/a	chr10:26986410-26986421 chr10:26986611-26986622
29	POLR2A	chr10:26985864-26987092	ProgFib	skin:	n/a	n/a
30	SP1	chr10:26985833-26986663	A549	lung:	n/a	chr10:26986339-26986353
31	MAX	chr10:26985939-26987379	Hela-S3	cervix:	n/a	chr10:26986852-26986863 chr10:26986851-26986866
32	UBTF	chr10:26986105-26987062	K562	blood:	n/a	n/a
33	STAT5A	chr10:26985860-26986756	GM12878	blood:	n/a	chr10:26986335-26986344 chr10:26986329-26986349 chr10:26986335-26986343 chr10:26986334-26986343 chr10:26986329-26986349
34	SIN3AK20	chr10:26985778-26987277	MCF-7	breast:	n/a	n/a
35	MAX	chr10:26985918-26987186	ECC-1	luminal epithelium:	n/a	chr10:26986852-26986863 chr10:26986851-26986866
36	POLR2A	chr10:26985960-26987063	HUVEC	blood vessel:	n/a	n/a
37	RFX5	chr10:26985944-26986675	Hela-S3	cervix:	n/a	n/a
38	HDAC2	chr10:26985869-26987076	MCF-7	breast:	n/a	n/a
39	POLR2A	chr10:26985839-26986832	GM12892	blood:	n/a	n/a
40	BCLAF1	chr10:26985935-26986722	GM12878	blood:	n/a	chr10:26986432-26986445 chr10:26986483-26986496
41	MYBL2	chr10:26986292-26987039	HepG2	liver:	n/a	n/a
42	ELK1	chr10:26986114-26986675	K562	blood:	n/a	n/a
43	PAX5	chr10:26986039-26986510	GM12891	blood:	n/a	chr10:26986094-26986112 chr10:26986066-26986076
44	POLR2A	chr10:26985608-26987220	GM12892	blood:	n/a	n/a
45	ZEB1	chr10:26986271-26986938	GM12878	blood:	n/a	n/a
46	ELF1	chr10:26986082-26987074	HepG2	liver:	n/a	chr10:26986333-26986342 chr10:26986153-26986162
47	POLR2A	chr10:26986122-26986857	IMR90	lung:	n/a	n/a
48	CEBPB	chr10:26985767-26986942	Hela-S3	cervix:	n/a	chr10:26986086-26986099 chr10:26986010-26986021 chr10:26985938-26985949
49	MYC	chr10:26985974-26987018	MCF-7	breast:	n/a	chr10:26986852-26986863 chr10:26986851-26986866
50	MYC	chr10:26986033-26986979	HUVEC	blood vessel:	n/a	chr10:26986852-26986863 chr10:26986851-26986866

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:26986312-26986362	GM12891	blood:	n/a
2	chr10:26986312-26986362	ProgFib	skin:	n/a
3	chr10:26986312-26986362	K562	blood:	n/a
4	chr10:26986312-26986362	GM19239	blood:	n/a
5	chr10:26986312-26986362	HRPEpiC	eye:	n/a
6	chr10:26986312-26986362	CMK	blood:	n/a
7	chr10:26986312-26986362	HAEpiC	amniotic membrane:	n/a
8	chr10:26986312-26986362	HUVEC	blood vessel:	n/a
9	chr10:26986312-26986362	PFSK-1	brain:	n/a
10	chr10:26986312-26986362	H1-hESC	embryonic stem cell:	embryo
11	chr10:26986312-26986362	BE2_C	brain:	n/a
12	chr10:26986312-26986362	HepG2	liver:	n/a
13	chr10:26986312-26986362	A549	lung:	n/a
14	chr10:26986312-26986362	T-47D	breast:	n/a
15	chr10:26986312-26986362	NT2-D1	testis:	n/a
16	chr10:26986312-26986362	HNPCEpiC	eye:	n/a
17	chr10:26986312-26986362	HRE	kidney:	n/a
18	chr10:26986312-26986362	HIPEpiC	eye:	n/a
19	chr10:26986312-26986362	HCF	heart:	n/a
20	chr10:26986312-26986362	MCF10A-Er-Src	breast:	n/a
21	chr10:26986312-26986362	PANC-1	pancreas:	n/a
22	chr10:26986312-26986362	HRCEpiC	kidney:	n/a
23	chr10:26986312-26986362	U87	brain:	n/a
24	chr10:26986312-26986362	HCM	heart:	n/a
25	chr10:26986312-26986362	GM12892	blood:	n/a
26	chr10:26986312-26986362	BJ	skin:	n/a
27	chr10:26986312-26986362	ovcar-3	ovarian:	n/a
28	chr10:26986312-26986362	NHBE	bronchial:	n/a
29	chr10:26986312-26986362	HL-60	blood:	n/a
30	chr10:26986312-26986362	NB4	blood:	n/a
31	chr10:26986312-26986362	SK-N-SH_RA	brain:	n/a
32	chr10:26986312-26986362	SK-N-SH	brain:	n/a
33	chr10:26986312-26986362	HCPEpiC	choroid plexus:	n/a
34	chr10:26986312-26986362	PrEC	prostate:	n/a
35	chr10:26986312-26986362	NH-A	brain:	n/a
36	chr10:26986312-26986362	RPTEC	kidney:	n/a
37	chr10:26986312-26986362	IMR90	lung:	fetal
38	chr10:26986312-26986362	AG09309	skin:	n/a
39	chr10:26986312-26986362	GM06990	blood:	n/a
40	chr10:26986312-26986362	HEK293	kidney:	embryo
41	chr10:26986312-26986362	HEEpiC	esophagus:	n/a
42	chr10:26986312-26986362	LNCaP	prostate:	n/a
43	chr10:26986312-26986362	Hela-S3	cervix:	n/a
44	chr10:26986312-26986362	NHDF-neo	bronchial:	n/a
45	chr10:26986312-26986362	AG10803	skin:	n/a
46	chr10:26986312-26986362	AG04450	lung:	fetal
47	chr10:26986312-26986362	MCF-7	breast:	n/a
48	chr10:26986312-26986362	SKMC	muscle:	n/a
49	chr10:26986312-26986362	Jurkat	blood:	n/a
50	chr10:26986312-26986362	Hepatocyte	liver:	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:26985323..26988042-chr10:27148387..27150466,3	MCF-7	breast:
2	chr10:26986021..26987940-chr10:27149008..27151636,2	MCF-7	breast:
3	chr10:26985640..26986465-chr5:82372961..82373834,2	Hela-S3	cervix:
4	chr10:26986018..26986729-chr5:147763063..147763851,2	MCF-7	breast:
5	chr10:26985918..26987566-chr10:27148462..27151237,2	K562	blood:
6	chr10:26985752..26988058-chr10:26992017..26994907,3	MCF-7	breast:
7	chr10:26986198..26989615-chr10:27022506..27024765,3	MCF-7	breast:
8	chr10:26985057..26986781-chr10:27006850..27009579,2	K562	blood:
9	chr10:26986066..26987689-chr10:27148181..27149962,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ABI1-7	chr10:26984020-26986554	NONHSAT011856

Variant related genes	Relation type
PDSS1	TF binding region
PDSS1	CpG island
ENSG00000247199	Chromatin interaction
ENSG00000148459	Chromatin interaction
ENSG00000174695	Chromatin interaction
ENSG00000152422	Chromatin interaction
ENSG00000136754	Chromatin interaction
ENSG00000145868	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11015223	0.85[ASN][1000 genomes]
rs11015232	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12254548	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12415035	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1809359	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1960383	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3808913	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68159164	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7069431	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7100327	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71483808	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7896301	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7904343	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894975	chr10:26343356-27014467	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv3415799	chr10:26929831-27233591	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv1798973	chr10:26968171-27001814	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv550233	chr10:26968171-27011323	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26985400-26988600	Active TSS	GM12878-XiMat	blood
2	chr10:26985600-26986400	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr10:26985600-26987000	Active TSS	Colonic Mucosa	Colon
4	chr10:26985600-26987200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:26985600-26987200	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr10:26985600-26987200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr10:26985600-26987200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr10:26985600-26987200	Active TSS	Colon Smooth Muscle	Colon
9	chr10:26985600-26987200	Active TSS	Fetal Brain Male	brain
10	chr10:26985600-26987200	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr10:26985600-26987200	Active TSS	Right Atrium	heart
12	chr10:26985600-26987200	Active TSS	Right Ventricle	heart
13	chr10:26985600-26987200	Active TSS	NH-A	brain
14	chr10:26985600-26987200	Active TSS	NHLF	lung
15	chr10:26985600-26987400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr10:26985600-26987400	Active TSS	Fetal Kidney	kidney
17	chr10:26985600-26987600	Active TSS	H1 Cell Line	embryonic stem cell
18	chr10:26985600-26987600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr10:26985600-26987600	Active TSS	Fetal Muscle Trunk	muscle
20	chr10:26985600-26987800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr10:26985600-26987800	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr10:26985600-26988000	Active TSS	H9 Cell Line	embryonic stem cell
23	chr10:26985600-26988200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr10:26985600-26988200	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr10:26985600-26988200	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr10:26985600-26988200	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr10:26985600-26988200	Active TSS	A549	lung
28	chr10:26985600-26988400	Active TSS	Psoas Muscle	Psoas
29	chr10:26985800-26986400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr10:26985800-26986600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
31	chr10:26985800-26987000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr10:26985800-26987200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr10:26985800-26987200	Active TSS	Aorta	Aorta
34	chr10:26985800-26987200	Active TSS	Brain Angular Gyrus	brain
35	chr10:26985800-26987200	Active TSS	Gastric	stomach
36	chr10:26985800-26987200	Active TSS	Lung	lung
37	chr10:26985800-26987200	Active TSS	Pancreas	Pancrea
38	chr10:26985800-26987400	Active TSS	Fetal Intestine Small	intestine
39	chr10:26985800-26987400	Active TSS	Small Intestine	intestine
40	chr10:26985800-26987600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr10:26985800-26987600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr10:26985800-26987600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr10:26985800-26987600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr10:26985800-26987600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr10:26985800-26987600	Active TSS	Esophagus	oesophagus
46	chr10:26985800-26987600	Active TSS	Fetal Heart	heart
47	chr10:26985800-26987800	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr10:26985800-26988000	Active TSS	Thymus	Thymus
49	chr10:26986000-26987000	Active TSS	Primary T cells from cord blood	blood
50	chr10:26986000-26987000	Active TSS	Primary T helper naive cells from peripheral blood	blood

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