Variant report

Variant	rs2873310
Chromosome Location	chr16:81072145-81072146
allele	A/C
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	CEBPB	chr16:81072114-81072337	A549	lung:	n/a	chr16:81072199-81072210 chr16:81072197-81072214
2	CEBPB	chr16:81072043-81072367	HepG2	liver:	n/a	chr16:81072199-81072210 chr16:81072197-81072214
3	CEBPB	chr16:81072052-81072364	K562	blood:	n/a	chr16:81072199-81072210 chr16:81072197-81072214
4	CEBPB	chr16:81072038-81072362	IMR90	lung:	n/a	chr16:81072199-81072210 chr16:81072197-81072214
5	CEBPB	chr16:81072072-81072307	Hela-S3	cervix:	n/a	chr16:81072199-81072210 chr16:81072197-81072214

No.	Distal block	Cell Line	Cell type
1	chr16:81067084..81072191-chr16:81106033..81112629,21	MCF-7	breast:
2	chr16:81070898..81072766-chr16:81109747..81111312,2	MCF-7	breast:
3	chr16:81037151..81042784-chr16:81066438..81073797,14	K562	blood:
4	chr16:81068310..81071293-chr16:81072010..81074075,3	K562	blood:
5	chr16:81039321..81041372-chr16:81071649..81073188,2	K562	blood:

Variant related genes	Relation type
ATMIN	TF binding region
ENSG00000260213	TF binding region
ENSG00000166454	Chromatin interaction
ENSG00000260213	Chromatin interaction
ENSG00000166455	Chromatin interaction
ENSG00000103121	Chromatin interaction
ENSG00000166451	Chromatin interaction
ENSG00000245059	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11150337	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11863158	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11865207	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12927239	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12927828	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12928556	0.81[ASN][1000 genomes]
rs12929903	0.81[ASN][1000 genomes]
rs12935418	0.89[ASN][1000 genomes]
rs13185	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2257378	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2278025	0.82[ASN][1000 genomes]
rs2549895	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2549896	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2549899	0.92[EUR][1000 genomes]
rs2602402	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2602404	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2602407	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2602431	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970076	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35096487	0.80[EUR][1000 genomes]
rs4889225	0.81[ASN][1000 genomes]
rs4889229	0.82[ASN][1000 genomes]
rs4889230	0.82[ASN][1000 genomes]
rs62054589	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7203546	0.81[ASN][1000 genomes]
rs7206814	0.83[ASN][1000 genomes]
rs804885	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs804896	0.84[ASN][1000 genomes]
rs804902	0.84[ASN][1000 genomes]
rs804904	0.85[ASN][1000 genomes]
rs804905	0.85[ASN][1000 genomes]
rs889516	0.86[ASN][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	nsv948534	chr16:80867635-81160492	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1065258	chr16:80887483-81081768	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv1064164	chr16:80918138-81126967	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv542991	chr16:80918138-81126967	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats 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	71 gene(s)	inside rSNPs	diseases
6	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	nsv573338	chr16:81020393-81106944	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv427984	chr16:81026691-81320341	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv995083	chr16:81050917-81076406	Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv1062724	chr16:81052312-81137007	Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1897	chr16:81060566-81105260	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	esv2422360	chr16:81066033-81180727	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2873310	GCSH	cis	Muscle Skeletal	GTEx
rs2873310	GCSH///LOC654085///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs2873310	ATMIN	cis	Muscle Skeletal	GTEx
rs2873310	CENPN	Cis_1M	lymphoblastoid	RTeQTL
rs2873310	GCSH///LOC730107	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81070400-81072600	Weak transcription	Esophagus	oesophagus
2	chr16:81070600-81072400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr16:81070600-81072600	Enhancers	Primary T cells fromperipheralblood	blood
4	chr16:81070600-81072800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr16:81070600-81073800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr16:81070600-81075800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr16:81070800-81072200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr16:81070800-81072400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr16:81070800-81072400	Enhancers	Colon Smooth Muscle	Colon
10	chr16:81070800-81072400	Genic enhancers	Fetal Stomach	stomach
11	chr16:81070800-81072600	Enhancers	Pancreas	Pancrea
12	chr16:81070800-81073400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr16:81070800-81073800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr16:81070800-81081800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr16:81071000-81072200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr16:81071000-81072200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr16:81071000-81072600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr16:81071000-81072800	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr16:81071000-81072800	Genic enhancers	Left Ventricle	heart
20	chr16:81071000-81074000	Weak transcription	Primary B cells from cord blood	blood
21	chr16:81071000-81074600	Enhancers	Brain Substantia Nigra	brain
22	chr16:81071000-81074600	Weak transcription	HSMM	muscle
23	chr16:81071000-81075200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr16:81071000-81075200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr16:81071000-81075400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr16:81071000-81075400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr16:81071000-81075800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr16:81071000-81076400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr16:81071000-81079800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr16:81071200-81072200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr16:81071200-81072200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr16:81071200-81072200	Enhancers	Brain Anterior Caudate	brain
33	chr16:81071200-81072200	Enhancers	Placenta	Placenta
34	chr16:81071200-81072400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr16:81071200-81072400	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr16:81071200-81072600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr16:81071200-81072600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr16:81071200-81072600	Weak transcription	Gastric	stomach
39	chr16:81071200-81072600	Weak transcription	GM12878-XiMat	blood
40	chr16:81071200-81072800	Strong transcription	Fetal Intestine Small	intestine
41	chr16:81071200-81073000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr16:81071200-81073000	Weak transcription	Fetal Brain Female	brain
43	chr16:81071200-81073400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr16:81071200-81073400	Weak transcription	NH-A	brain
45	chr16:81071200-81073600	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr16:81071200-81073600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr16:81071200-81073800	Weak transcription	Fetal Thymus	thymus
48	chr16:81071200-81073800	Weak transcription	Small Intestine	intestine
49	chr16:81071200-81074000	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr16:81071200-81074000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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