Variant report

Variant	rs35341359
Chromosome Location	chr3:112994937-112994938
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	CTCF	chr3:112994740-112995030	HFF-Myc	foreskin:	n/a	chr3:112994791-112994804 chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
2	NR3C1	chr3:112994767-112995287	ECC-1	luminal epithelium:	n/a	n/a
3	CTCF	chr3:112994820-112994970	SAEC	small airway:	n/a	chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
4	CTCF	chr3:112994587-112994985	H1-hESC	embryonic stem cell:	n/a	chr3:112994791-112994804 chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
5	MAZ	chr3:112994926-112995079	K562	blood:	n/a	n/a
6	RAD21	chr3:112994589-112995046	HepG2	liver:	n/a	chr3:112994830-112994844 chr3:112994835-112994844 chr3:112994826-112994845
7	EBF1	chr3:112994913-112995310	GM12878	blood:	n/a	n/a
8	ARID3A	chr3:112994883-112995237	HepG2	liver:	n/a	chr3:112995046-112995061
9	CTCF	chr3:112994800-112994950	HRE	kidney:	n/a	chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
10	RAD21	chr3:112994578-112995020	H1-hESC	embryonic stem cell:	n/a	chr3:112994830-112994844 chr3:112994835-112994844 chr3:112994826-112994845
11	CTCF	chr3:112994800-112994950	AG09319	gingival:	n/a	chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
12	CTCF	chr3:112994662-112994961	HepG2	liver:	n/a	chr3:112994791-112994804 chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
13	MAX	chr3:112994657-112995412	ECC-1	luminal epithelium:	n/a	chr3:112994794-112994804
14	CTCF	chr3:112994820-112994970	HCPEpiC	choroid plexus:	n/a	chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
15	CTCF	chr3:112994800-112994950	HMF	breast:	n/a	chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
16	CTCF	chr3:112994920-112995070	HCT-116	colon:	n/a	n/a
17	SPI1	chr3:112994871-112995720	GM12878	blood:	n/a	chr3:112995530-112995539 chr3:112995265-112995274
18	CTCF	chr3:112994800-112994950	HMEC	breast:	n/a	chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
19	CTCF	chr3:112994840-112994990	GM12875	blood:	n/a	n/a
20	CTCF	chr3:112994840-112994990	AG04449	skin:	n/a	n/a
21	ZBTB7A	chr3:112994468-112995482	ECC-1	luminal epithelium:	n/a	n/a
22	CTCF	chr3:112994820-112994970	AG09319	gingival:	n/a	chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
23	CTCF	chr3:112994631-112994969	HepG2	liver:	n/a	chr3:112994791-112994804 chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
24	RAD21	chr3:112994504-112995386	ECC-1	luminal epithelium:	n/a	chr3:112994830-112994844 chr3:112995281-112995294 chr3:112994835-112994844 chr3:112994826-112994845 chr3:112995288-112995302
25	CTCF	chr3:112994820-112994970	HAc	cerebellar:	n/a	chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
26	CTCF	chr3:112994820-112994970	HRPEpiC	eye:	n/a	chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
27	CTCF	chr3:112994820-112994970	GM12871	blood:	n/a	chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
28	POLR2A	chr3:112994906-112995372	U87	brain:	n/a	n/a
29	CTCF	chr3:112994800-112994950	MCF-7	breast:	n/a	chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
30	CTCF	chr3:112994920-112995070	GM12872	blood:	n/a	n/a
31	CTCF	chr3:112994820-112994970	HPF	lung:	n/a	chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
32	CTCF	chr3:112994800-112994950	NHDF-neo	bronchial:	n/a	chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
33	RAD21	chr3:112994650-112995173	H1-hESC	embryonic stem cell:	n/a	chr3:112994830-112994844 chr3:112994835-112994844 chr3:112994826-112994845
34	RUNX3	chr3:112994916-112995332	GM12878	blood:	n/a	n/a
35	CTCF	chr3:112994840-112994990	BJ	skin:	n/a	n/a
36	CTCF	chr3:112994840-112994990	HBMEC	blood vessel:	n/a	n/a
37	RAD21	chr3:112994625-112995088	SK-N-SH_RA	brain:	n/a	chr3:112994830-112994844 chr3:112994835-112994844 chr3:112994826-112994845
38	RCOR1	chr3:112994841-112995153	K562	blood:	n/a	n/a
39	RAD21	chr3:112994655-112995044	IMR90	lung:	n/a	chr3:112994830-112994844 chr3:112994835-112994844 chr3:112994826-112994845
40	CTCF	chr3:112994820-112994970	HCFaa	heart:	n/a	chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
41	MAX	chr3:112994669-112995391	ECC-1	luminal epithelium:	n/a	chr3:112994794-112994804
42	RAD21	chr3:112994717-112994955	SK-N-SH_RA	brain:	n/a	chr3:112994830-112994844 chr3:112994835-112994844 chr3:112994826-112994845
43	RAD21	chr3:112994695-112994973	HepG2	liver:	n/a	chr3:112994830-112994844 chr3:112994835-112994844 chr3:112994826-112994845
44	NFIC	chr3:112994595-112995396	ECC-1	luminal epithelium:	n/a	n/a
45	CTCF	chr3:112994820-112994970	AG10803	skin:	n/a	chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
46	CTCF	chr3:112994900-112995050	GM12874	blood:	n/a	n/a
47	ESR1	chr3:112994708-112995256	ECC-1	luminal epithelium:	n/a	n/a
48	ESR1	chr3:112994626-112995270	ECC-1	luminal epithelium:	n/a	n/a
49	NFIC	chr3:112994547-112995381	ECC-1	luminal epithelium:	n/a	n/a
50	EP300	chr3:112994691-112995500	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:112854694..112855593-chr3:112994517..112995397,2	MCF-7	breast:
2	chr3:112854651..112855751-chr3:112994357..112995381,6	MCF-7	breast:
3	chr3:112770020..112770678-chr3:112994428..112995328,4	MCF-7	breast:
4	chr3:112994340..112996390-chr3:112999455..113002856,3	MCF-7	breast:
5	chr3:112769779..112770713-chr3:112994422..112995284,3	MCF-7	breast:

Variant related genes	Relation type
BOC	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs13093350	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094203	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650100	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34239722	0.86[EUR][1000 genomes]
rs41271355	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56163361	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66518523	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs775227	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808951	0.83[EUR][1000 genomes];0.97[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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112969000-112995200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr3:112973600-112997200	Weak transcription	Colonic Mucosa	Colon
3	chr3:112983800-112995000	Weak transcription	Lung	lung
4	chr3:112984800-112998400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:112987800-112996000	Enhancers	Pancreas	Pancrea
7	chr3:112988000-113003000	Strong transcription	Placenta Amnion	Placenta Amnion
8	chr3:112988400-112996800	Weak transcription	Placenta	Placenta
9	chr3:112989000-112997000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:112990400-113036000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:112990600-113004000	Weak transcription	NHEK	skin
12	chr3:112991600-112995000	Weak transcription	Aorta	Aorta
13	chr3:112991600-112995000	Weak transcription	K562	blood
14	chr3:112991800-112995000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:112991800-113006400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:112992400-112995200	Genic enhancers	Fetal Muscle Leg	muscle
17	chr3:112992800-112995000	Genic enhancers	Fetal Muscle Trunk	muscle
18	chr3:112993000-112995600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:112993000-112996200	Enhancers	Fetal Thymus	thymus
20	chr3:112993000-112997000	Weak transcription	Fetal Intestine Small	intestine
21	chr3:112993400-112995800	Enhancers	Fetal Brain Male	brain
22	chr3:112993400-112996200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:112993400-112996800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:112993400-112997400	Genic enhancers	Fetal Stomach	stomach
25	chr3:112993600-112995000	Enhancers	Brain Cingulate Gyrus	brain
26	chr3:112993600-112995000	Enhancers	Fetal Brain Female	brain
27	chr3:112993600-112995000	Enhancers	HMEC	breast
28	chr3:112993600-112995600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:112993600-112995800	Enhancers	Fetal Kidney	kidney
30	chr3:112993600-112996200	Genic enhancers	Fetal Lung	lung
31	chr3:112993800-112996400	Enhancers	Brain Angular Gyrus	brain
32	chr3:112993800-112997000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:112993800-113036000	Weak transcription	Right Ventricle	heart
34	chr3:112994000-112995000	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr3:112994000-112995000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:112994000-112995000	Enhancers	Brain Germinal Matrix	brain
37	chr3:112994000-112995000	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr3:112994000-112995200	Enhancers	Primary B cells from peripheral blood	blood
39	chr3:112994000-112995400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:112994000-112995400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:112994000-112995800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:112994000-112995800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:112994200-112995000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:112994200-112995000	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr3:112994200-112995000	Enhancers	Stomach Mucosa	stomach
46	chr3:112994200-112995000	Enhancers	GM12878-XiMat	blood
47	chr3:112994200-112995200	Enhancers	H1 Cell Line	embryonic stem cell
48	chr3:112994200-112995200	Enhancers	Fetal Intestine Large	intestine
49	chr3:112994200-112995400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:112994200-112995600	Enhancers	iPS-20b Cell Line	embryonic stem cell

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