Variant report

Variant	rs13407036
Chromosome Location	chr2:97578150-97578151
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:97523464..97526230-chr2:97576942..97579887,2	K562	blood:
2	chr2:97575476..97578400-chr2:97584018..97588039,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213337	Chromatin interaction
ENSG00000163126	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10191663	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11888101	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1320147	0.86[CEU][hapmap]
rs13403225	0.86[CEU][hapmap]
rs17119655	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs17119656	0.94[CEU][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes]
rs2314651	0.87[EUR][1000 genomes]
rs28612110	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4260285	0.93[EUR][1000 genomes]
rs58984980	0.92[EUR][1000 genomes]
rs59131346	0.93[EUR][1000 genomes]
rs59660613	0.94[EUR][1000 genomes]
rs60621865	0.80[AMR][1000 genomes]
rs62152901	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62152903	0.92[EUR][1000 genomes]
rs62152904	0.94[EUR][1000 genomes]
rs62152905	0.93[EUR][1000 genomes]
rs62152906	0.93[EUR][1000 genomes]
rs62152907	0.94[EUR][1000 genomes]
rs62152908	0.94[EUR][1000 genomes]
rs62152910	0.94[EUR][1000 genomes]
rs6576990	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs6717064	0.93[CEU][hapmap];0.95[EUR][1000 genomes]
rs6718420	0.94[EUR][1000 genomes]
rs6721921	0.93[CEU][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes]
rs6734673	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs6751815	0.90[EUR][1000 genomes]
rs72811651	0.93[EUR][1000 genomes]
rs7572852	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7574488	0.86[CEU][hapmap]
rs7589232	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs7591775	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7592101	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7603256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
10	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
11	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
rs13407036	FAM178B	cis	Esophagus Muscularis	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97572400-97579200	Enhancers	Fetal Brain Male	brain
2	chr2:97573800-97579000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:97574000-97578200	Weak transcription	Esophagus	oesophagus
4	chr2:97574000-97578200	Weak transcription	Fetal Thymus	thymus
5	chr2:97574000-97578600	Weak transcription	Placenta	Placenta
6	chr2:97574000-97582000	Weak transcription	Colonic Mucosa	Colon
7	chr2:97574200-97578200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr2:97574200-97578400	Weak transcription	Pancreas	Pancrea
9	chr2:97575400-97579200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:97575600-97581600	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:97575800-97578600	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:97575800-97581800	Weak transcription	Right Atrium	heart
13	chr2:97576000-97578800	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr2:97576000-97581600	Weak transcription	Brain Substantia Nigra	brain
15	chr2:97576200-97578200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:97576400-97578200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:97576800-97578400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:97576800-97578600	Enhancers	Primary T cells fromperipheralblood	blood
19	chr2:97576800-97578600	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr2:97576800-97580600	Enhancers	Left Ventricle	heart
21	chr2:97577000-97578400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr2:97577000-97578600	Enhancers	Fetal Brain Female	brain
23	chr2:97577000-97580600	Enhancers	Right Ventricle	heart
24	chr2:97577200-97578200	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr2:97577200-97578600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr2:97577200-97578600	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr2:97577200-97578800	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr2:97577200-97580200	Bivalent Enhancer	Fetal Muscle Leg	muscle
29	chr2:97577200-97589600	Weak transcription	Fetal Heart	heart
30	chr2:97577400-97578200	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr2:97577400-97578400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:97577400-97578600	Enhancers	H1 Cell Line	embryonic stem cell
33	chr2:97577400-97578600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:97577400-97579000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
35	chr2:97577400-97579000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr2:97577400-97579200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:97577400-97579200	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr2:97577400-97580600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:97577600-97578200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:97577600-97578200	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr2:97577600-97578200	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr2:97577600-97578200	Enhancers	Primary T cells from cord blood	blood
43	chr2:97577600-97578600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr2:97577600-97578600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr2:97577600-97579000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:97577600-97579000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:97577600-97579000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:97577600-97579200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
49	chr2:97577600-97579200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr2:97577600-97579600	Active TSS	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links