Variant report

Variant	rs4885634
Chromosome Location	chr13:80056907-80056908
allele	C/T
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	POLR2A	chr13:80054410-80058154	MCF10A-Er-Src	breast:	n/a	n/a
2	CEBPB	chr13:80056441-80056980	IMR90	lung:	n/a	n/a
3	POLR2A	chr13:80054586-80058161	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:79977332..79980292-chr13:80055643..80057700,2	K562	blood:
2	chr13:80056153..80058862-chr13:80062367..80066425,4	K562	blood:
3	chr13:79979196..79982246-chr13:80054691..80057070,3	MCF-7	breast:

Variant related genes	Relation type
NDFIP2-AS1	TF binding region
ENSG00000227354	Chromatin interaction
ENSG00000139746	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1208049	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1212082	0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1335368	0.82[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs1335370	0.82[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs1408049	0.81[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs1414155	0.89[ASN][1000 genomes]
rs1414156	0.89[ASN][1000 genomes]
rs1475797	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1577416	0.93[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1577418	0.82[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs1748761	0.80[JPT][hapmap]
rs2065743	0.91[ASN][1000 genomes]
rs2265377	0.85[JPT][hapmap]
rs2476172	0.81[ASN][1000 genomes]
rs2476173	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2484343	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2484344	0.81[ASN][1000 genomes]
rs2484345	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2760101	0.90[ASN][1000 genomes]
rs2760102	0.92[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2760103	0.88[ASN][1000 genomes]
rs2760105	0.82[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2760106	0.81[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs2763809	0.80[JPT][hapmap]
rs2783119	0.93[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2783120	0.92[ASN][1000 genomes]
rs2783121	0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs2783122	0.81[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs2783125	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2783126	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs314687	0.84[ASN][1000 genomes]
rs314688	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3742117	0.81[CHB][hapmap]
rs3742119	0.85[CEU][hapmap]
rs386603	0.85[ASN][1000 genomes]
rs3903388	0.82[CEU][hapmap]
rs4145207	0.96[ASN][1000 genomes]
rs4476060	0.87[ASN][1000 genomes]
rs4885633	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4885636	0.82[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs6563110	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6563113	0.93[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563115	0.92[ASN][1000 genomes]
rs6563116	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs700396	0.88[ASN][1000 genomes]
rs7321953	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73235963	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7325095	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7328494	0.85[JPT][hapmap]
rs7338530	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7339303	0.93[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7982263	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7987193	0.80[JPT][hapmap]
rs7988601	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7990344	0.93[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs7996493	0.94[ASN][1000 genomes]
rs8001281	0.80[JPT][hapmap]
rs8002042	0.93[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9318626	0.89[CEU][hapmap]
rs9318627	0.84[CEU][hapmap]
rs9318644	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9530922	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9530925	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9545086	0.82[CEU][hapmap]
rs9545087	0.82[CEU][hapmap]
rs9545097	0.82[CEU][hapmap]
rs9545101	0.81[AMR][1000 genomes]
rs9545142	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9565510	0.82[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs9574418	0.81[AMR][1000 genomes]
rs9574422	0.82[CEU][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes]
rs9574429	0.87[ASN][1000 genomes]
rs9574434	0.82[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs9593396	0.89[CEU][hapmap];0.81[AMR][1000 genomes]
rs9593399	0.87[ASN][1000 genomes]
rs9601240	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9601242	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs987284	0.93[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832657	chr13:79904978-80099108	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv523979	chr13:79979679-80120263	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4885634	RBM26	Cis_1M	lymphoblastoid	RTeQTL
rs4885634	RP11-25J23.3	cis	Thyroid	GTEx
rs4885634	RP11-25J23.3	cis	lung	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80054800-80057000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr13:80054800-80057000	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr13:80054800-80057000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr13:80054800-80057000	Active TSS	Right Atrium	heart
5	chr13:80054800-80057000	Active TSS	K562	blood
6	chr13:80054800-80057200	Active TSS	Colonic Mucosa	Colon
7	chr13:80054800-80057200	Active TSS	Rectal Smooth Muscle	rectum
8	chr13:80054800-80057400	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr13:80054800-80057600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr13:80054800-80057800	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr13:80054800-80057800	Active TSS	Fetal Intestine Large	intestine
12	chr13:80054800-80057800	Active TSS	Fetal Intestine Small	intestine
13	chr13:80054800-80058000	Active TSS	Duodenum Mucosa	Duodenum
14	chr13:80054800-80059400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr13:80055000-80057000	Active TSS	Osteobl	bone
16	chr13:80055000-80057200	Active TSS	HSMMtube	muscle
17	chr13:80055000-80057400	Active TSS	Esophagus	oesophagus
18	chr13:80055000-80057600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr13:80055200-80057200	Active TSS	HMEC	breast
20	chr13:80055200-80057400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr13:80055200-80057400	Active TSS	NHEK	skin
22	chr13:80055600-80057200	Active TSS	Dnd41	blood
23	chr13:80055800-80057200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr13:80055800-80057800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr13:80056000-80058800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr13:80056200-80057000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr13:80056200-80057200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr13:80056200-80057200	Weak transcription	Brain Substantia Nigra	brain
29	chr13:80056200-80057200	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr13:80056200-80057400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr13:80056200-80057600	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr13:80056200-80057800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr13:80056200-80058000	Enhancers	Stomach Mucosa	stomach
34	chr13:80056200-80058000	Flanking Active TSS	NH-A	brain
35	chr13:80056200-80058800	Weak transcription	Small Intestine	intestine
36	chr13:80056200-80059200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr13:80056200-80060600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr13:80056200-80060800	Weak transcription	Gastric	stomach
39	chr13:80056200-80063200	Weak transcription	Left Ventricle	heart
40	chr13:80056200-80066400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr13:80056200-80066600	Weak transcription	Psoas Muscle	Psoas
42	chr13:80056200-80077400	Weak transcription	Right Ventricle	heart
43	chr13:80056400-80057000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr13:80056400-80057000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
45	chr13:80056400-80057000	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr13:80056400-80057400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr13:80056400-80057400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr13:80056400-80057400	Flanking Active TSS	GM12878-XiMat	blood
49	chr13:80056400-80057600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr13:80056400-80057800	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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