Variant report

Variant	rs62152903
Chromosome Location	chr2:97570377-97570378
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97554940..97556485-chr2:97567959..97570783,2	K562	blood:
2	chr2:97568240..97570833-chr2:97573049..97574563,2	K562	blood:
3	chr2:97562141..97565511-chr2:97568458..97571207,4	K562	blood:
4	chr2:97568349..97571105-chr2:97578253..97580296,2	K562	blood:
5	chr2:97569777..97572197-chr2:97574930..97577007,2	K562	blood:

Variant related genes	Relation type
ENSG00000168754	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10191663	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11888101	0.97[EUR][1000 genomes]
rs13407036	0.92[EUR][1000 genomes]
rs17119655	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17119656	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2314651	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28612110	0.97[EUR][1000 genomes]
rs4260285	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57675226	0.95[ASN][1000 genomes]
rs58984980	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59131346	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59660613	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62152871	0.95[ASN][1000 genomes]
rs62152901	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62152902	0.98[ASN][1000 genomes]
rs62152904	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62152905	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62152906	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62152907	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62152908	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62152910	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6576990	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6717064	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6718420	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6721921	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6734673	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6735969	0.95[ASN][1000 genomes]
rs6751815	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72811651	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7572852	0.92[EUR][1000 genomes]
rs7589232	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7591775	0.88[EUR][1000 genomes]
rs7592101	0.91[EUR][1000 genomes]
rs7603256	0.97[EUR][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62152903	FAM178B	cis	Esophagus Muscularis	GTEx
rs62152903	FAM178B	cis	Artery Tibial	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97558200-97572200	Weak transcription	Right Atrium	heart
2	chr2:97561600-97572200	Weak transcription	Psoas Muscle	Psoas
3	chr2:97561800-97572000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:97562000-97572200	Weak transcription	Gastric	stomach
5	chr2:97562400-97572000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:97562400-97572000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr2:97563400-97575200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:97563800-97572200	Weak transcription	Brain Angular Gyrus	brain
9	chr2:97563800-97573200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr2:97564200-97572200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr2:97565000-97572000	Weak transcription	Right Ventricle	heart
12	chr2:97565000-97572000	Weak transcription	HSMMtube	muscle
13	chr2:97565000-97575000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:97565200-97572000	Weak transcription	Fetal Lung	lung
15	chr2:97565200-97572200	Weak transcription	Ovary	ovary
16	chr2:97565400-97572200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:97566600-97572200	Weak transcription	Esophagus	oesophagus
18	chr2:97568200-97570600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:97568400-97571200	Enhancers	Colon Smooth Muscle	Colon
20	chr2:97569000-97570600	Enhancers	K562	blood
21	chr2:97569600-97572000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:97569600-97572000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:97569600-97572000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:97569600-97572000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:97569600-97572000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:97569600-97572200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr2:97569600-97572200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:97569600-97572200	Weak transcription	Colonic Mucosa	Colon
29	chr2:97569800-97572000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:97569800-97572200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr2:97569800-97572400	Weak transcription	Brain Anterior Caudate	brain
32	chr2:97569800-97572400	Weak transcription	Fetal Thymus	thymus
33	chr2:97569800-97572400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr2:97569800-97573200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:97569800-97573200	Weak transcription	Fetal Brain Female	brain
36	chr2:97570000-97570400	Enhancers	Stomach Smooth Muscle	stomach
37	chr2:97570000-97571800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr2:97570000-97571800	Weak transcription	Fetal Stomach	stomach
39	chr2:97570000-97571800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:97570000-97572000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:97570000-97572000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr2:97570000-97572000	Weak transcription	Placenta	Placenta
43	chr2:97570000-97572000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr2:97570000-97572200	Weak transcription	Brain Hippocampus Middle	brain
45	chr2:97570000-97572200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr2:97570000-97572200	Weak transcription	Spleen	Spleen
47	chr2:97570000-97572400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr2:97570000-97573800	Enhancers	Fetal Muscle Leg	muscle
49	chr2:97570000-97575000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr2:97570000-97575400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links