Variant report

Variant	rs878936
Chromosome Location	chr13:52405251-52405252
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52403949..52406430-chr13:52408338..52410301,2	K562	blood:
2	chr13:52402539..52404938-chr13:52405246..52407174,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10220242	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12584414	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12585859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2031994	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4354822	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4941713	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4943028	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56401568	0.94[ASN][1000 genomes]
rs621221	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7992588	0.86[CHB][hapmap]
rs9535767	0.86[JPT][hapmap]
rs9591433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9596586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9596587	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9634846	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs975504	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv455884	chr13:52302630-52405251	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv561644	chr13:52302630-52405251	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv455887	chr13:52318522-52405251	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv561645	chr13:52318522-52405251	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs878936	C13orf1	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52393600-52406200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr13:52393600-52418600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr13:52400800-52406400	Weak transcription	GM12878-XiMat	blood
4	chr13:52401200-52407600	Weak transcription	Lung	lung
5	chr13:52401600-52419200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr13:52401800-52406200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr13:52401800-52406600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr13:52402200-52406200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr13:52402400-52406000	Weak transcription	Fetal Heart	heart
10	chr13:52402600-52406200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr13:52402600-52406200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr13:52402600-52406200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr13:52402800-52406200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr13:52402800-52406200	Weak transcription	Left Ventricle	heart
15	chr13:52402800-52412800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr13:52404000-52406200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr13:52404000-52406200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr13:52404000-52406400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr13:52404200-52406000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr13:52404400-52410200	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr13:52404600-52406000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr13:52404600-52406000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr13:52404600-52406200	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr13:52404600-52406200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr13:52404600-52406200	Weak transcription	Fetal Thymus	thymus
26	chr13:52404600-52406400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr13:52404800-52405800	Weak transcription	Primary T cells from cord blood	blood
28	chr13:52404800-52406000	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr13:52404800-52406000	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr13:52404800-52406200	Weak transcription	Primary B cells from cord blood	blood
31	chr13:52404800-52413800	Weak transcription	Fetal Intestine Small	intestine
32	chr13:52405000-52406200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr13:52405200-52405600	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr13:52405200-52405600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr13:52405200-52406200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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