Variant report

Variant	rs62152906
Chromosome Location	chr2:97572270-97572271
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97559950..97563991-chr2:97572149..97576823,4	K562	blood:
2	chr2:97572260..97573823-chr2:97580585..97582287,2	MCF-7	breast:
3	chr2:97542354..97544469-chr2:97571292..97573499,2	K562	blood:
4	chr2:97481675..97483983-chr2:97572049..97574143,2	MCF-7	breast:
5	chr2:97570898..97573698-chr2:97588276..97590943,2	K562	blood:

Variant related genes	Relation type
ENSG00000168763	Chromatin interaction
ENSG00000168754	Chromatin interaction

Extended variants
information (count: 46 )
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	0.94[EUR][1000 genomes]
rs13407036	0.93[EUR][1000 genomes]
rs17119655	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17119656	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2314651	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28612110	0.94[EUR][1000 genomes]
rs4260285	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57675226	0.94[ASN][1000 genomes]
rs58984980	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59131346	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59660613	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62152871	0.94[ASN][1000 genomes]
rs62152901	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62152902	0.97[ASN][1000 genomes]
rs62152903	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62152904	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62152905	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62152907	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62152908	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62152910	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6576990	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6717064	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6718420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721921	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6734673	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6735969	0.94[ASN][1000 genomes]
rs6751815	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72811651	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7572852	0.93[EUR][1000 genomes]
rs7589232	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7591775	0.89[EUR][1000 genomes]
rs7592101	0.92[EUR][1000 genomes]
rs7603256	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv582497	chr2:97569305-97715154	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
12	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62152906	FAM178B	cis	Esophagus Muscularis	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97563400-97575200	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr2:97563800-97573200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:97565000-97575000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr2:97569800-97572400	Weak transcription	Brain Anterior Caudate	brain
5	chr2:97569800-97572400	Weak transcription	Fetal Thymus	thymus
6	chr2:97569800-97572400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:97569800-97573200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:97569800-97573200	Weak transcription	Fetal Brain Female	brain
9	chr2:97570000-97572400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:97570000-97573800	Enhancers	Fetal Muscle Leg	muscle
11	chr2:97570000-97575000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr2:97570000-97575400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:97570200-97575000	Weak transcription	Primary T cells from cord blood	blood
14	chr2:97571800-97572600	Enhancers	Fetal Muscle Trunk	muscle
15	chr2:97571800-97572800	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr2:97571800-97574400	Enhancers	Fetal Stomach	stomach
17	chr2:97572000-97572400	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr2:97572000-97572400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:97572000-97572400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:97572000-97572400	Enhancers	Duodenum Mucosa	Duodenum
21	chr2:97572000-97572600	Enhancers	NHDF-Ad	bronchial
22	chr2:97572000-97572800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:97572000-97572800	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr2:97572000-97572800	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr2:97572000-97572800	Flanking Active TSS	Colon Smooth Muscle	Colon
26	chr2:97572000-97573000	Enhancers	Right Ventricle	heart
27	chr2:97572000-97573400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:97572000-97573800	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr2:97572000-97573800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:97572000-97573800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:97572000-97573800	Enhancers	Fetal Heart	heart
32	chr2:97572000-97574000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:97572000-97574000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr2:97572000-97574000	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr2:97572000-97574000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:97572000-97574000	Enhancers	Fetal Lung	lung
37	chr2:97572000-97574000	Enhancers	Placenta	Placenta
38	chr2:97572000-97574400	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr2:97572000-97576000	Enhancers	Brain Substantia Nigra	brain
40	chr2:97572000-97576200	Enhancers	Brain Cingulate Gyrus	brain
41	chr2:97572200-97572400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:97572200-97572400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:97572200-97572400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:97572200-97572400	Enhancers	Gastric	stomach
45	chr2:97572200-97572400	Enhancers	Psoas Muscle	Psoas
46	chr2:97572200-97572400	Enhancers	HSMM	muscle
47	chr2:97572200-97572600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:97572200-97572800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:97572200-97572800	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr2:97572200-97573000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum

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