Variant report

Variant	rs16970287
Chromosome Location	chr15:79228257-79228258
allele	A/G
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	chr15:79227446-79228446	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:79222916-79228963	GM12891	blood:	n/a	n/a
3	POLR2A	chr15:79222914-79229026	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:79224751..79228848-chr15:79235939..79238870,4	MCF-7	breast:
2	chr15:79216646..79219513-chr15:79226461..79228629,2	MCF-7	breast:
3	chr15:79222672..79226174-chr15:79226685..79229932,5	K562	blood:
4	chr15:79224120..79226402-chr15:79226596..79229872,4	MCF-7	breast:

Variant related genes	Relation type
CTSH	TF binding region
ENSG00000103811	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10152868	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10444811	0.87[YRI][hapmap]
rs12050510	0.87[YRI][hapmap]
rs12050511	0.88[YRI][hapmap]
rs12440862	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12441725	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12443105	0.88[YRI][hapmap]
rs16970344	0.83[JPT][hapmap]
rs1836556	0.89[YRI][hapmap]
rs2289695	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2289697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2289698	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2289700	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs3784537	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3784538	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3784540	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3825931	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58119858	0.94[EUR][1000 genomes]
rs60888706	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60944855	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7161986	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7163828	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7182836	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73470389	0.94[EUR][1000 genomes]
rs8034542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8039683	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9302286	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33573	chr15:79053484-79293881	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs16970287	MORF4L1	cis	multi-tissue	Pritchard
rs16970287	MORF4L1	cis	Liver	GTEx
rs16970287	CSK	cis	cerebellum	SCAN
rs16970287	CTSH	Cis_1M	lymphoblastoid	RTeQTL
rs16970287	MORF4L1	cis	parietal	SCAN
rs16970287	MORF4L1	cis	cerebellum	SCAN
rs16970287	C15orf17	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79199800-79229400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr15:79203600-79231000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr15:79210400-79230200	Strong transcription	Fetal Intestine Large	intestine
4	chr15:79213400-79228400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr15:79214600-79229400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr15:79215400-79233200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr15:79215400-79236600	Weak transcription	Small Intestine	intestine
8	chr15:79215600-79229400	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr15:79215600-79232800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr15:79215800-79229600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr15:79217200-79229400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr15:79219400-79229400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr15:79219400-79229600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:79219600-79236200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:79219800-79229400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:79220200-79229200	Weak transcription	Dnd41	blood
17	chr15:79220200-79229600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr15:79220200-79229600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr15:79220200-79230600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:79220200-79231800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr15:79220200-79235200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr15:79220600-79229400	Weak transcription	Primary T cells from cord blood	blood
23	chr15:79220600-79236200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr15:79220600-79236400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:79221200-79229400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr15:79222000-79232000	Strong transcription	HepG2	liver
27	chr15:79222200-79233400	Weak transcription	Thymus	Thymus
28	chr15:79222400-79236400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:79223600-79228600	Weak transcription	Fetal Thymus	thymus
30	chr15:79223600-79229400	Weak transcription	HUVEC	blood vessel
31	chr15:79223800-79236000	Weak transcription	HSMMtube	muscle
32	chr15:79223800-79236200	Weak transcription	Brain Angular Gyrus	brain
33	chr15:79224000-79229600	Weak transcription	Brain Substantia Nigra	brain
34	chr15:79224200-79230200	Strong transcription	Pancreas	Pancrea
35	chr15:79224200-79236400	Weak transcription	Colonic Mucosa	Colon
36	chr15:79224400-79231000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr15:79224400-79236600	Weak transcription	HMEC	breast
38	chr15:79224600-79236200	Weak transcription	Psoas Muscle	Psoas
39	chr15:79225000-79229400	Weak transcription	Stomach Mucosa	stomach
40	chr15:79225600-79236400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:79226400-79236000	Weak transcription	Fetal Kidney	kidney
42	chr15:79226600-79229000	Genic enhancers	Monocytes-CD14+_RO01746	blood
43	chr15:79226600-79236200	Weak transcription	Rectal Smooth Muscle	rectum
44	chr15:79226800-79228800	Genic enhancers	Primary monocytes fromperipheralblood	blood
45	chr15:79226800-79229400	Weak transcription	Ovary	ovary
46	chr15:79227000-79229200	Strong transcription	Fetal Stomach	stomach
47	chr15:79227000-79229600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr15:79227000-79229600	Weak transcription	Right Atrium	heart
49	chr15:79227000-79236000	Weak transcription	Colon Smooth Muscle	Colon
50	chr15:79227200-79229400	Enhancers	Primary B cells from cord blood	blood

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