Variant report

Variant	rs7860518
Chromosome Location	chr9:94826465-94826466
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	chr9:94805829..94808024-chr9:94825130..94827991,2	K562	blood:
2	chr9:94821053..94823320-chr9:94823986..94826593,3	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10512220	0.86[JPT][hapmap]
rs10739925	0.86[JPT][hapmap]
rs10761143	0.86[JPT][hapmap]
rs10820936	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10820937	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992221	0.90[CEU][hapmap];0.86[MEX][hapmap]
rs10992234	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12340044	0.81[JPT][hapmap]
rs1892268	0.86[JPT][hapmap]
rs1970121	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.90[ASN][1000 genomes]
rs2297568	0.86[JPT][hapmap]
rs28727560	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2895201	0.86[JPT][hapmap]
rs3847308	0.89[JPT][hapmap]
rs4307406	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58129324	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6479399	0.88[ASW][hapmap];0.90[LWK][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.84[AFR][1000 genomes]
rs6479400	0.86[JPT][hapmap]
rs6479403	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7020136	0.86[JPT][hapmap]
rs7024583	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029539	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7041193	0.86[JPT][hapmap]
rs7042102	0.81[JPT][hapmap]
rs7046540	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7848874	0.86[JPT][hapmap]
rs7852067	0.90[CEU][hapmap]
rs7856177	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7858659	0.91[CEU][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.84[AMR][1000 genomes]
rs7863564	0.89[EUR][1000 genomes]
rs7866702	0.84[EUR][1000 genomes]
rs7869504	0.86[JPT][hapmap]
rs7871444	0.86[JPT][hapmap]
rs7872515	0.90[CEU][hapmap];0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv831653	chr9:94692454-94867542	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	esv3324084	chr9:94821393-94830399	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
7	esv3482528	chr9:94821472-94830365	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
8	esv3482529	chr9:94821472-94830365	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7860518	SPTLC1	cis	parietal	SCAN
rs7860518	FBP1	cis	parietal	SCAN
rs7860518	OMD	cis	cerebellum	SCAN
rs7860518	ZNF484	cis	parietal	SCAN
rs7860518	CDK20	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94810800-94860200	Weak transcription	Right Ventricle	heart
2	chr9:94811800-94828400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr9:94812200-94832200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:94812400-94828400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:94817600-94827000	Weak transcription	Small Intestine	intestine
6	chr9:94817600-94828000	Weak transcription	Gastric	stomach
7	chr9:94817600-94828000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr9:94817600-94828200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:94817600-94828400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:94817600-94828600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr9:94817800-94826800	Weak transcription	HSMMtube	muscle
12	chr9:94817800-94827000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr9:94817800-94877000	Weak transcription	Fetal Heart	heart
14	chr9:94818400-94827200	Weak transcription	HSMM	muscle
15	chr9:94818400-94828400	Weak transcription	Esophagus	oesophagus
16	chr9:94820600-94844400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:94821000-94827200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:94821000-94828200	Weak transcription	Aorta	Aorta
19	chr9:94821200-94828400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:94821400-94826800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr9:94821400-94827200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr9:94821400-94829800	Weak transcription	HMEC	breast
23	chr9:94822000-94827400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:94822200-94829600	Weak transcription	K562	blood
25	chr9:94822200-94832600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr9:94822400-94827000	Weak transcription	Ovary	ovary
27	chr9:94822400-94827400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:94822400-94860200	Weak transcription	Stomach Mucosa	stomach
29	chr9:94822600-94826600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:94822600-94826800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr9:94822600-94827000	Weak transcription	Left Ventricle	heart
32	chr9:94822600-94827000	Weak transcription	Thymus	Thymus
33	chr9:94822600-94827200	Strong transcription	NH-A	brain
34	chr9:94822600-94827400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr9:94822600-94827800	Weak transcription	Fetal Stomach	stomach
36	chr9:94822600-94827800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr9:94822600-94828000	Weak transcription	Spleen	Spleen
38	chr9:94822600-94828200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr9:94822600-94828200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:94822600-94828200	Weak transcription	Lung	lung
41	chr9:94823000-94827800	Weak transcription	Pancreas	Pancrea
42	chr9:94823200-94826800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
43	chr9:94823200-94826800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
44	chr9:94823200-94826800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
45	chr9:94823200-94828200	Weak transcription	Fetal Intestine Small	intestine
46	chr9:94823200-94828600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
47	chr9:94823200-94842800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr9:94823200-94844400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr9:94823400-94826800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr9:94823400-94826800	ZNF genes & repeats	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links