Variant report

Variant	rs35670704
Chromosome Location	chr2:113384302-113384303
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	RAD21	chr2:113384109-113384403	GM12878	blood:	n/a	chr2:113384356-113384368 chr2:113384276-113384289 chr2:113384278-113384290 chr2:113384273-113384292 chr2:113384278-113384288
2	POLR2A	chr2:113384084-113384425	HCT-116	colon:	n/a	n/a
3	CTCF	chr2:113384180-113384330	AG10803	skin:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290
4	CTCF	chr2:113384139-113384438	A549	lung:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290 chr2:113384422-113384435
5	YY1	chr2:113384064-113384451	ECC-1	luminal epithelium:	n/a	chr2:113384298-113384310 chr2:113384297-113384316
6	CTCF	chr2:113384220-113384370	GM12875	blood:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290
7	CTCF	chr2:113384180-113384330	AG09319	gingival:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290
8	FOXM1	chr2:113383903-113384570	GM12878	blood:	n/a	n/a
9	CTCF	chr2:113384056-113384462	K562	blood:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290 chr2:113384422-113384435
10	MYBL2	chr2:113384047-113384615	HepG2	liver:	n/a	n/a
11	ARID3A	chr2:113384221-113384432	HepG2	liver:	n/a	n/a
12	CTCF	chr2:113384161-113384382	SK-N-SH_RA	brain:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290
13	CTCF	chr2:113384180-113384330	GM12864	blood:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290
14	CTCF	chr2:113384160-113384310	HFF	foreskin:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290
15	ZNF143	chr2:113384106-113384494	GM12878	blood:	n/a	n/a
16	CTCF	chr2:113384161-113384418	A549	lung:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290
17	CTCF	chr2:113384059-113384532	GM12878	blood:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290 chr2:113384422-113384435
18	MAZ	chr2:113384145-113384589	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr2:113384101-113385305	IMR90	lung:	n/a	n/a
20	CTCF	chr2:113384200-113384350	RPTEC	kidney:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290
21	RCOR1	chr2:113384117-113385294	Hela-S3	cervix:	n/a	n/a
22	BACH1	chr2:113384052-113384440	H1-hESC	embryonic stem cell:	n/a	n/a
23	HCFC1	chr2:113384148-113384445	K562	blood:	n/a	n/a
24	ZNF384	chr2:113384157-113384357	K562	blood:	n/a	n/a
25	CHD1	chr2:113384203-113384327	GM12878	blood:	n/a	n/a
26	BCLAF1	chr2:113384065-113384471	GM12878	blood:	n/a	n/a
27	FOXM1	chr2:113384055-113384548	GM12878	blood:	n/a	n/a
28	CTCF	chr2:113384200-113384350	HPAF	blood vessel:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290
29	SMC3	chr2:113384079-113384544	K562	blood:	n/a	chr2:113384274-113384288 chr2:113384392-113384399 chr2:113384424-113384432
30	POU2F2	chr2:113384035-113384505	GM12878	blood:	n/a	n/a
31	TEAD4	chr2:113384025-113385431	SK-N-SH	brain:	n/a	n/a
32	CTCF	chr2:113384220-113384370	GM12874	blood:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290
33	POU2F2	chr2:113384084-113384506	GM12891	blood:	n/a	n/a
34	CTCF	chr2:113384155-113384427	GM19239	blood:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290
35	CTCF	chr2:113384147-113384415	K562	blood:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290
36	TCF12	chr2:113384123-113384419	GM12878	blood:	n/a	n/a
37	MAZ	chr2:113384111-113384468	K562	blood:	n/a	n/a
38	CTCF	chr2:113384164-113384408	GM20000	blood:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290
39	RAD21	chr2:113384125-113384464	K562	blood:	n/a	chr2:113384356-113384368 chr2:113384276-113384289 chr2:113384278-113384290 chr2:113384273-113384292 chr2:113384278-113384288
40	CTCF	chr2:113384200-113384350	GM12873	blood:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290
41	SP4	chr2:113384094-113384329	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr2:113384160-113384310	GM12865	blood:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290
43	ZC3H11A	chr2:113384164-113384395	K562	blood:	n/a	n/a
44	CTCF	chr2:113384160-113384310	A549	lung:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290
45	CTCF	chr2:113384200-113384350	NHLF	lung:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290
46	RCOR1	chr2:113384157-113384472	HepG2	liver:	n/a	n/a
47	MAX	chr2:113384143-113384428	Hela-S3	cervix:	n/a	n/a
48	CTCF	chr2:113384141-113384449	NHEK	skin:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290 chr2:113384422-113384435
49	CTCF	chr2:113384143-113384439	Fibrobl	skin:	n/a	chr2:113384275-113384288 chr2:113384274-113384295 chr2:113384272-113384290 chr2:113384422-113384435
50	TFAP2C	chr2:113384122-113385417	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:113383684..113385667-chr2:113481537..113485469,35	K562	blood:
2	chr2:113381929..113384460-chr2:113482679..113485995,5	MCF-7	breast:
3	chr2:113382749..113384471-chr2:113464194..113466806,2	K562	blood:
4	chr2:113378841..113381519-chr2:113383348..113385320,2	MCF-7	breast:
5	chr16:15187795..15188622-chr2:113384234..113385184,2	Hela-S3	cervix:
6	chr2:113383343..113387238-chr2:113388797..113391596,3	MCF-7	breast:
7	chr2:113379636..113386577-chr2:113398111..113406278,16	MCF-7	breast:
8	chr2:113340704..113344392-chr2:113381565..113384382,5	MCF-7	breast:
9	chr2:113383746..113384937-chr2:113484019..113484887,5	MCF-7	breast:
10	chr2:113383790..113384739-chr2:113448337..113449101,4	MCF-7	breast:
11	chr2:113380240..113386960-chr2:113401832..113406779,10	MCF-7	breast:
12	chr2:113383817..113384789-chr2:113484041..113484921,7	MCF-7	breast:
13	chr2:113380970..113385799-chr2:113479613..113484625,8	K562	blood:
14	chr2:113384015..113385213-chr2:113482175..113483476,11	MCF-7	breast:
15	chr2:113383314..113385378-chr2:113441903..113443465,2	MCF-7	breast:
16	chr2:113382212..113385648-chr2:113390770..113393800,3	MCF-7	breast:
17	chr2:113383706..113386562-chr2:113417388..113419756,2	MCF-7	breast:
18	chr2:113384187..113384849-chr2:113482175..113483114,3	MCF-7	breast:
19	chr2:113361529..113363513-chr2:113383774..113386118,3	K562	blood:
20	chr2:113380843..113384962-chr2:113480402..113484110,5	K562	blood:
21	chr2:113383765..113384740-chr2:113448133..113449127,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231747	TF binding region
ENSG00000144130	Chromatin interaction
ENSG00000125611	Chromatin interaction
ENSG00000231747	Chromatin interaction
ENSG00000144136	Chromatin interaction
ENSG00000260735	Chromatin interaction
ENSG00000237753	Chromatin interaction
ENSG00000085721	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11900874	0.86[EUR][1000 genomes]
rs12987250	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13025131	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13030884	0.85[EUR][1000 genomes]
rs17586834	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17587043	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17647292	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28819453	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34015418	0.99[EUR][1000 genomes]
rs36082214	1.00[EUR][1000 genomes]
rs3980072	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3980074	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4405766	0.86[EUR][1000 genomes]
rs6716749	0.88[EUR][1000 genomes]
rs6716762	0.88[EUR][1000 genomes]
rs6737981	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71414685	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7566777	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7607685	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7607817	0.85[AMR][1000 genomes];0.98[EUR][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	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv470480	chr2:113373950-113429752	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs35670704	AC079922.3	cis	Esophagus Muscularis	GTEx
rs35670704	AC079922.3	cis	Esophagus Mucosa	GTEx
rs35670704	AC079922.3	cis	Whole Blood	GTEx
rs35670704	AC079922.3	cis	Heart Left Ventricle	GTEx
rs35670704	AC079922.3	cis	Artery Aorta	GTEx
rs35670704	AC079922.3	cis	Thyroid	GTEx
rs35670704	AC079922.3	cis	Muscle Skeletal	GTEx
rs35670704	AC079922.3	cis	Artery Tibial	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113372400-113388600	Weak transcription	Gastric	stomach
2	chr2:113372800-113388000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:113379800-113387600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:113380200-113387600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:113380400-113387600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:113380800-113388400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:113381000-113384400	Enhancers	NHLF	lung
8	chr2:113381400-113388400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:113381600-113386000	Enhancers	Primary hematopoietic stem cells	blood
10	chr2:113381600-113388200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:113381600-113389600	Enhancers	Placenta	Placenta
12	chr2:113381800-113385200	Flanking Active TSS	Hela-S3	cervix
13	chr2:113382000-113385800	Enhancers	Placenta Amnion	Placenta Amnion
14	chr2:113382200-113384400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:113382400-113387600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:113382600-113384400	Weak transcription	Stomach Mucosa	stomach
17	chr2:113383000-113384400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:113383000-113385200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:113383200-113384600	Enhancers	Fetal Brain Male	brain
20	chr2:113383200-113384800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:113383400-113385000	Flanking Active TSS	HMEC	breast
22	chr2:113383400-113386000	Enhancers	Fetal Thymus	thymus
23	chr2:113383400-113386200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:113383600-113385800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:113383600-113385800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr2:113383600-113385800	Enhancers	K562	blood
27	chr2:113383600-113386000	Enhancers	Primary B cells from cord blood	blood
28	chr2:113383800-113385000	Enhancers	Primary B cells from peripheral blood	blood
29	chr2:113383800-113385800	Enhancers	Fetal Muscle Leg	muscle
30	chr2:113384000-113384400	Enhancers	Fetal Muscle Trunk	muscle
31	chr2:113384000-113384800	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr2:113384000-113384800	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr2:113384000-113385000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:113384000-113385200	Flanking Active TSS	A549	lung
35	chr2:113384000-113385200	Flanking Active TSS	NH-A	brain
36	chr2:113384000-113385200	Flanking Active TSS	Osteobl	bone
37	chr2:113384000-113385600	Flanking Active TSS	HSMM	muscle
38	chr2:113384000-113385800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr2:113384000-113386000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr2:113384000-113386000	Enhancers	Small Intestine	intestine
41	chr2:113384000-113386000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr2:113384200-113384400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:113384200-113384400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr2:113384200-113384400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr2:113384200-113384400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:113384200-113384400	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr2:113384200-113384600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr2:113384200-113384600	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr2:113384200-113384600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
50	chr2:113384200-113384600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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