Variant report

Variant	rs10220242
Chromosome Location	chr13:52397614-52397615
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52389100..52392374-chr13:52395474..52400602,4	MCF-7	breast:
2	chr13:52376742..52378303-chr13:52397197..52399197,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102796	Chromatin interaction

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

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

rs_ID	r²[population]
rs12584414	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12585859	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2031994	0.90[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap]
rs4354822	0.91[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs4941713	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4943028	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56401568	0.96[ASN][1000 genomes]
rs621221	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7992588	0.86[CHB][hapmap]
rs878936	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]
rs9535767	0.86[JPT][hapmap]
rs9591433	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9596586	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9596587	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9634846	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[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
rs10220242	C13orf1	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52389600-52398200	Weak transcription	Brain Substantia Nigra	brain
2	chr13:52390200-52398200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr13:52392400-52404800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr13:52392600-52399600	Weak transcription	Fetal Lung	lung
5	chr13:52392800-52401800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr13:52393200-52397800	Enhancers	Fetal Muscle Leg	muscle
7	chr13:52393600-52406200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:52393600-52418600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr13:52393800-52397800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr13:52393800-52398600	Weak transcription	Colon Smooth Muscle	Colon
11	chr13:52393800-52399200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr13:52393800-52399200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr13:52393800-52399200	Weak transcription	Adipose Nuclei	Adipose
14	chr13:52393800-52400000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr13:52394000-52399000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr13:52394000-52399000	Weak transcription	Right Atrium	heart
17	chr13:52394000-52399400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr13:52394000-52399600	Weak transcription	Left Ventricle	heart
19	chr13:52394000-52399800	Weak transcription	Right Ventricle	heart
20	chr13:52394200-52397800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr13:52394200-52399000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr13:52394200-52399800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr13:52394400-52398000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr13:52394600-52400200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
25	chr13:52394800-52397800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
26	chr13:52395200-52397800	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr13:52395200-52399200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr13:52395800-52397800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
29	chr13:52396000-52397800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr13:52396000-52398400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
31	chr13:52396000-52399200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr13:52396000-52400000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr13:52396200-52398400	Enhancers	Brain Anterior Caudate	brain
34	chr13:52396400-52399200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr13:52396600-52398000	Enhancers	Primary B cells from peripheral blood	blood
36	chr13:52396600-52398200	Enhancers	Primary hematopoietic stem cells	blood
37	chr13:52396600-52399600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr13:52396600-52400400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr13:52396600-52404000	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr13:52396600-52404600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr13:52396800-52397800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr13:52396800-52399000	Weak transcription	GM12878-XiMat	blood
43	chr13:52397000-52398600	Active TSS	Thymus	Thymus
44	chr13:52397000-52399200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr13:52397000-52400200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr13:52397200-52398000	Enhancers	Primary B cells from cord blood	blood
47	chr13:52397200-52399600	Enhancers	HSMM	muscle
48	chr13:52397400-52399000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr13:52397400-52399000	Weak transcription	Small Intestine	intestine
50	chr13:52397400-52400400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links