Variant report

Variant	rs3814401
Chromosome Location	chr3:112997141-112997142
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	chr3:112997120-112997270	GM12869	blood:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
2	CTCF	chr3:112997139-112997389	K562	blood:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
3	CTCF	chr3:112997120-112997270	HEEpiC	esophagus:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
4	CTCF	chr3:112997120-112997270	GM12868	blood:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
5	CTCF	chr3:112997122-112997347	MCF-7	breast:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
6	RAD21	chr3:112997124-112997278	HepG2	liver:	n/a	chr3:112997229-112997248
7	CTCF	chr3:112996991-112997456	MCF-7	breast:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
8	CTCF	chr3:112997080-112997230	HCT-116	colon:	n/a	n/a
9	RAD21	chr3:112997035-112997433	H1-hESC	embryonic stem cell:	n/a	chr3:112997229-112997248
10	TCF12	chr3:112997057-112997341	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr3:112997140-112997359	MCF-7	breast:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
12	CTCF	chr3:112997140-112997290	HAc	cerebellar:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
13	SMC3	chr3:112997073-112997386	GM12878	blood:	n/a	chr3:112997233-112997247
14	CTCF	chr3:112997120-112997270	SAEC	small airway:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
15	CTCF	chr3:112997140-112997290	GM12875	blood:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
16	CTCF	chr3:112997100-112997250	Hela-S3	cervix:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
17	RAD21	chr3:112996942-112997460	H1-hESC	embryonic stem cell:	n/a	chr3:112997229-112997248
18	CTCF	chr3:112997120-112997270	AoAF	blood vessel:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
19	CTCF	chr3:112997140-112997290	HPAF	blood vessel:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
20	CTCF	chr3:112997140-112997290	GM12872	blood:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
21	CTCF	chr3:112997028-112997413	H1-hESC	embryonic stem cell:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
22	CTCF	chr3:112997120-112997270	HepG2	liver:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
23	CTCF	chr3:112997140-112997290	AG09309	skin:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
24	CTCF	chr3:112997140-112997290	GM12867	blood:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
25	RAD21	chr3:112996938-112997522	MCF-7	breast:	n/a	chr3:112997229-112997248
26	CTCF	chr3:112997120-112997270	HEK293	kidney:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
27	CTCF	chr3:112997120-112997270	HA-sp	spinal cord:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
28	CTCF	chr3:112997080-112997230	HRPEpiC	eye:	n/a	n/a
29	CTCF	chr3:112997115-112997353	MCF-7	breast:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
30	RAD21	chr3:112997017-112997343	SK-N-SH_RA	brain:	n/a	chr3:112997229-112997248
31	CTCF	chr3:112997120-112997270	GM12870	blood:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
32	CTCF	chr3:112997081-112997349	A549	lung:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
33	CTCF	chr3:112997093-112997394	GM12878	blood:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
34	CTCF	chr3:112997110-112997383	GM12892	blood:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
35	CTCF	chr3:112997120-112997270	HRPEpiC	eye:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
36	CTCF	chr3:112997140-112997290	GM12864	blood:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
37	CTCF	chr3:112997060-112997290	NHDF-neo	bronchial:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
38	CTCF	chr3:112997120-112997270	HMEC	breast:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
39	RAD21	chr3:112997024-112997433	H1-hESC	embryonic stem cell:	n/a	chr3:112997229-112997248
40	CTCF	chr3:112997086-112997377	GM12891	blood:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
41	CTCF	chr3:112997134-112997359	MCF-7	breast:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
42	CTCF	chr3:112997140-112997290	HBMEC	blood vessel:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
43	CTCF	chr3:112997140-112997290	HFF-Myc	foreskin:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
44	CTCF	chr3:112997100-112997250	SAEC	small airway:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
45	CTCF	chr3:112997140-112997290	HA-sp	spinal cord:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
46	RAD21	chr3:112997000-112997423	A549	lung:	n/a	chr3:112997229-112997248
47	CTCF	chr3:112997088-112997374	GM19238	blood:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
48	RAD21	chr3:112996964-112997402	A549	lung:	n/a	chr3:112997229-112997248
49	CTCF	chr3:112997106-112997424	GM19239	blood:	n/a	chr3:112997233-112997246 chr3:112997231-112997249 chr3:112997226-112997247
50	RAD21	chr3:112997124-112997344	GM12878	blood:	n/a	chr3:112997229-112997248

No.	Distal block	Cell Line	Cell type
1	chr3:112995543..112998104-chr3:113010327..113013877,3	MCF-7	breast:
2	chr3:112854981..112855803-chr3:112996965..112997651,4	MCF-7	breast:
3	chr3:112855072..112855606-chr3:112996550..112997471,2	MCF-7	breast:
4	chr3:112769762..112770724-chr3:112996830..112997711,9	MCF-7	breast:
5	chr3:112986625..112989851-chr3:112997054..112999009,3	MCF-7	breast:
6	chr3:112769775..112770734-chr3:112996923..112997769,3	MCF-7	breast:

Variant related genes	Relation type
BOC	TF binding region
ENSG00000206530	Chromatin interaction
ENSG00000144857	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11923623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11929678	0.81[CEU][hapmap]
rs16860704	0.92[EUR][1000 genomes]
rs16860739	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16860784	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860788	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17255413	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs17320507	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3814405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41374946	1.00[EUR][1000 genomes]
rs55681309	1.00[EUR][1000 genomes]
rs55681380	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55744928	0.82[EUR][1000 genomes]
rs55888075	1.00[EUR][1000 genomes]
rs55969905	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56130902	1.00[EUR][1000 genomes]
rs7614288	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs775221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3814401	BOC	cis	multi-tissue	Pritchard

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112973600-112997200	Weak transcription	Colonic Mucosa	Colon
2	chr3:112984800-112998400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:112988000-113003000	Strong transcription	Placenta Amnion	Placenta Amnion
5	chr3:112990400-113036000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:112990600-113004000	Weak transcription	NHEK	skin
7	chr3:112991800-113006400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:112993400-112997400	Genic enhancers	Fetal Stomach	stomach
9	chr3:112993800-113036000	Weak transcription	Right Ventricle	heart
10	chr3:112994200-112997800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:112994800-112997400	Weak transcription	Gastric	stomach
12	chr3:112995200-112999400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:112995200-113001200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:112995200-113016000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:112995200-113022400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:112995400-112998200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:112995400-113006000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:112995400-113006200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:112995400-113024000	Weak transcription	Aorta	Aorta
20	chr3:112995400-113035800	Weak transcription	Lung	lung
21	chr3:112995600-112997200	Enhancers	Spleen	Spleen
22	chr3:112995600-112998200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr3:112995600-113006400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:112995600-113008400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:112995800-112997200	Enhancers	Brain Substantia Nigra	brain
26	chr3:112995800-112997400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:112995800-112997400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:112995800-112997400	Enhancers	Brain Anterior Caudate	brain
29	chr3:112995800-112998400	Enhancers	Primary B cells from peripheral blood	blood
30	chr3:112995800-112998400	Genic enhancers	Fetal Muscle Trunk	muscle
31	chr3:112995800-112999400	Weak transcription	Fetal Kidney	kidney
32	chr3:112995800-112999600	Weak transcription	HSMMtube	muscle
33	chr3:112995800-113004000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:112995800-113006600	Weak transcription	Fetal Brain Male	brain
35	chr3:112995800-113013000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:112995800-113035800	Weak transcription	Thymus	Thymus
37	chr3:112996000-112997400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:112996000-112997800	Weak transcription	Brain Germinal Matrix	brain
39	chr3:112996000-112998000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr3:112996000-113000000	Weak transcription	Pancreas	Pancrea
41	chr3:112996000-113005800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:112996000-113025400	Weak transcription	Small Intestine	intestine
43	chr3:112996200-112997400	Genic enhancers	Stomach Smooth Muscle	stomach
44	chr3:112996200-112997800	Enhancers	Brain Hippocampus Middle	brain
45	chr3:112996200-112997800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr3:112996200-112998400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:112996200-112999400	Weak transcription	Fetal Thymus	thymus
48	chr3:112996200-113000400	Weak transcription	Stomach Mucosa	stomach
49	chr3:112996200-113000400	Strong transcription	NHDF-Ad	bronchial
50	chr3:112996200-113001200	Strong transcription	Fetal Lung	lung

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