Variant report

Variant	rs899746
Chromosome Location	chr15:83520582-83520583
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	RCOR1	chr15:83520572-83521430	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:83517113..83521654-chr15:83652714..83657006,7	MCF-7	breast:
2	chr15:83519425..83521228-chr15:83661730..83663571,2	K562	blood:

Variant related genes	Relation type
HOMER2	TF binding region
ENSG00000103942	Chromatin interaction
ENSG00000169612	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12442119	0.94[ASW][hapmap];0.95[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1256424	0.82[ASW][hapmap];0.94[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs1256426	0.89[YRI][hapmap]
rs1256447	0.83[MKK][hapmap]
rs12594415	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17294229	1.00[YRI][hapmap]
rs2251275	0.85[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2667377	0.87[LWK][hapmap];0.86[MKK][hapmap];0.94[YRI][hapmap]
rs2667378	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2667379	0.82[AFR][1000 genomes]
rs3784376	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3784377	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55633961	0.80[AFR][1000 genomes]
rs750234	0.85[MKK][hapmap];0.94[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs899746	WHAMM	cis	cerebellum	SCAN
rs899746	BTBD1	cis	parietal	SCAN
rs899746	ANKRD34C	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83504600-83549400	Weak transcription	Psoas Muscle	Psoas
2	chr15:83505800-83520800	Weak transcription	Dnd41	blood
3	chr15:83505800-83522400	Weak transcription	Fetal Kidney	kidney
4	chr15:83506000-83524200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:83506200-83527400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:83506200-83543800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:83507200-83539400	Weak transcription	Fetal Intestine Small	intestine
8	chr15:83507800-83521800	Weak transcription	Brain Germinal Matrix	brain
9	chr15:83513200-83532000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:83514200-83521600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:83514400-83542800	Weak transcription	Primary T cells from cord blood	blood
12	chr15:83516000-83523400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:83517800-83522800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr15:83518200-83522600	Enhancers	Fetal Brain Female	brain
15	chr15:83518200-83523000	Enhancers	Fetal Thymus	thymus
16	chr15:83518400-83522800	Enhancers	Fetal Brain Male	brain
17	chr15:83518600-83522400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:83518800-83520800	Weak transcription	Primary B cells from cord blood	blood
19	chr15:83518800-83521000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr15:83518800-83524200	Weak transcription	Lung	lung
21	chr15:83519000-83521200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr15:83519000-83521200	Weak transcription	Osteobl	bone
23	chr15:83519000-83521800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr15:83519000-83523400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr15:83519000-83524200	Weak transcription	Left Ventricle	heart
26	chr15:83519000-83524400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr15:83519000-83524600	Weak transcription	Adipose Nuclei	Adipose
28	chr15:83519000-83524800	Weak transcription	Right Atrium	heart
29	chr15:83519000-83535800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr15:83519000-83541400	Weak transcription	Brain Anterior Caudate	brain
31	chr15:83519200-83520600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:83519200-83520600	Weak transcription	Fetal Stomach	stomach
33	chr15:83519200-83520600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr15:83519200-83521200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr15:83519200-83521400	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr15:83519200-83521800	Strong transcription	Liver	Liver
37	chr15:83519200-83522000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr15:83519200-83523400	Weak transcription	Colon Smooth Muscle	Colon
39	chr15:83519200-83524200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:83519200-83524200	Weak transcription	Right Ventricle	heart
41	chr15:83519200-83524400	Strong transcription	Gastric	stomach
42	chr15:83519200-83528800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr15:83519200-83536200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:83519400-83520600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:83519400-83520600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:83519400-83520600	Weak transcription	NH-A	brain
47	chr15:83519400-83521400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr15:83519400-83521600	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr15:83519400-83525800	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr15:83519600-83520800	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links