Variant report

Variant	rs62152901
Chromosome Location	chr2:97564898-97564899
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	STAT3	chr2:97564663-97565189	MCF10A-Er-Src	breast:	n/a	chr2:97564933-97564945
2	FOS	chr2:97564803-97565234	MCF10A-Er-Src	breast:	n/a	chr2:97564963-97564973 chr2:97565031-97565041
3	FOS	chr2:97564839-97565202	MCF10A-Er-Src	breast:	n/a	chr2:97564963-97564973 chr2:97565031-97565041
4	FOS	chr2:97564878-97565141	MCF10A-Er-Src	breast:	n/a	chr2:97564963-97564973 chr2:97565031-97565041
5	STAT3	chr2:97564821-97565178	MCF10A-Er-Src	breast:	n/a	chr2:97564933-97564945
6	FOS	chr2:97564803-97565242	MCF10A-Er-Src	breast:	n/a	chr2:97564963-97564973 chr2:97565031-97565041
7	TCF7L2	chr2:97564530-97564901	MCF-7	breast:	n/a	chr2:97564745-97564752 chr2:97564744-97564753
8	STAT3	chr2:97564760-97565234	MCF10A-Er-Src	breast:	n/a	chr2:97564933-97564945
9	MYC	chr2:97564883-97565157	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:97549904..97552223-chr2:97564807..97567554,3	K562	blood:
2	chr2:97559351..97562496-chr2:97564447..97568319,4	K562	blood:
3	chr2:97481720..97483625-chr2:97563695..97565331,2	MCF-7	breast:
4	chr2:97559983..97562569-chr2:97564469..97566255,2	K562	blood:

Variant related genes	Relation type
FAM178B	TF binding region
ENSG00000168754	Chromatin interaction
ENSG00000168763	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10191663	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11888101	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13407036	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17119655	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17119656	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2314651	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28612110	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4260285	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57675226	0.86[ASN][1000 genomes]
rs58984980	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59131346	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59660613	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62152871	0.86[ASN][1000 genomes]
rs62152902	0.86[ASN][1000 genomes]
rs62152903	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62152904	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62152905	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62152906	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62152907	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62152908	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62152910	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6576990	0.96[EUR][1000 genomes]
rs6717064	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6718420	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6721921	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6734673	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6735969	0.86[ASN][1000 genomes]
rs6751815	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72811651	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7572852	0.93[EUR][1000 genomes]
rs7589232	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7591775	0.89[EUR][1000 genomes]
rs7592101	0.92[EUR][1000 genomes]
rs7603256	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking 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 miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62152901	FAM178B	cis	Esophagus Muscularis	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97556400-97565200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr2:97556600-97566000	Enhancers	Fetal Thymus	thymus
3	chr2:97558200-97572200	Weak transcription	Right Atrium	heart
4	chr2:97558600-97566200	Enhancers	Fetal Muscle Leg	muscle
5	chr2:97559600-97565800	Enhancers	HSMM	muscle
6	chr2:97560600-97566600	Enhancers	Placenta	Placenta
7	chr2:97560800-97565400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:97561000-97565200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:97561000-97565400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:97561000-97565800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr2:97561200-97566800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:97561200-97566800	Enhancers	Spleen	Spleen
13	chr2:97561600-97565000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:97561600-97572200	Weak transcription	Psoas Muscle	Psoas
15	chr2:97561800-97572000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:97562000-97572200	Weak transcription	Gastric	stomach
17	chr2:97562200-97565600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:97562200-97569200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:97562400-97565400	Enhancers	Stomach Smooth Muscle	stomach
20	chr2:97562400-97569200	Weak transcription	Brain Substantia Nigra	brain
21	chr2:97562400-97569200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:97562400-97572000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:97562400-97572000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr2:97562600-97569200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr2:97562600-97569200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr2:97562600-97569200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr2:97562600-97569600	Weak transcription	Fetal Brain Female	brain
28	chr2:97562800-97565200	Enhancers	HMEC	breast
29	chr2:97563000-97566000	Enhancers	Lung	lung
30	chr2:97563200-97565200	Enhancers	Muscle Satellite Cultured Cells	--
31	chr2:97563200-97565400	Enhancers	Placenta Amnion	Placenta Amnion
32	chr2:97563200-97566000	Enhancers	Esophagus	oesophagus
33	chr2:97563400-97565000	Weak transcription	Ovary	ovary
34	chr2:97563400-97565400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:97563400-97569200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:97563400-97575200	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr2:97563600-97566200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr2:97563800-97572200	Weak transcription	Brain Angular Gyrus	brain
39	chr2:97563800-97573200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr2:97564200-97572200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr2:97564400-97565200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:97564400-97565200	Enhancers	Primary T cells from cord blood	blood
43	chr2:97564400-97565200	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr2:97564400-97565200	Enhancers	NHDF-Ad	bronchial
45	chr2:97564400-97565200	Enhancers	NHEK	skin
46	chr2:97564400-97565400	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr2:97564600-97565000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr2:97564600-97565000	Enhancers	Right Ventricle	heart
49	chr2:97564600-97565000	Enhancers	HSMMtube	muscle
50	chr2:97564600-97565200	Enhancers	Osteobl	bone

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