Variant report

Variant	rs10993052
Chromosome Location	chr9:96861798-96861799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96791853..96794356-chr9:96860367..96862558,2	MCF-7	breast:
2	chr9:96859686..96862226-chr9:96927604..96929691,2	K562	blood:
3	chr9:96861428..96863422-chr9:96927160..96928732,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269946	Chromatin interaction
ENSG00000158079	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10114320	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3847307	0.83[YRI][hapmap]
rs4282632	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744313	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7875583	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893589	chr9:96624645-96884544	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv482457	chr9:96813852-96996170	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	217 gene(s)	inside rSNPs	diseases
3	nsv1043704	chr9:96816552-96873018	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv831655	chr9:96834042-97042009	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	218 gene(s)	inside rSNPs	diseases
5	nsv893591	chr9:96849137-96883271	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	esv2761543	chr9:96857735-96875582	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10993052	SPTLC1	cis	parietal	SCAN
rs10993052	ZNF169	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96824200-96869600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr9:96828200-96862000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr9:96828200-96868200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr9:96829600-96872400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:96835400-96861800	Weak transcription	Primary B cells from cord blood	blood
6	chr9:96840200-96863600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:96845600-96885400	Weak transcription	Gastric	stomach
8	chr9:96846000-96870600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr9:96847800-96862600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:96848000-96863200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr9:96849000-96868800	Weak transcription	HepG2	liver
12	chr9:96849400-96866800	Weak transcription	Fetal Kidney	kidney
13	chr9:96849400-96869600	Weak transcription	HUVEC	blood vessel
14	chr9:96849400-96869800	Weak transcription	Colon Smooth Muscle	Colon
15	chr9:96849400-96883800	Weak transcription	Brain Germinal Matrix	brain
16	chr9:96849600-96870400	Weak transcription	Fetal Lung	lung
17	chr9:96849800-96864200	Weak transcription	Fetal Heart	heart
18	chr9:96850600-96870000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr9:96855400-96863200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:96856000-96863600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr9:96856400-96863600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr9:96857000-96863600	Weak transcription	Thymus	Thymus
23	chr9:96857200-96863600	Weak transcription	Fetal Thymus	thymus
24	chr9:96857200-96871000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr9:96857200-96882800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr9:96857400-96868600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr9:96857600-96862000	Strong transcription	Brain Anterior Caudate	brain
28	chr9:96857800-96865200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr9:96857800-96865400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr9:96858200-96865400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr9:96858400-96862600	Strong transcription	Fetal Stomach	stomach
32	chr9:96858400-96863600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr9:96858400-96865600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr9:96859200-96869600	Weak transcription	HSMMtube	muscle
35	chr9:96859200-96880800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr9:96859600-96864400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr9:96860000-96865400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr9:96860200-96864000	Weak transcription	Fetal Intestine Large	intestine
39	chr9:96860200-96870200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr9:96860200-96876200	Weak transcription	Esophagus	oesophagus
41	chr9:96860400-96865200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr9:96860400-96867400	Weak transcription	Dnd41	blood
43	chr9:96860400-96873400	Weak transcription	NHLF	lung
44	chr9:96860600-96862400	Weak transcription	Brain Substantia Nigra	brain
45	chr9:96860600-96867000	Weak transcription	Psoas Muscle	Psoas
46	chr9:96860600-96870000	Weak transcription	A549	lung
47	chr9:96860600-96870600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr9:96860600-96870800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr9:96860600-96871000	Weak transcription	Brain Angular Gyrus	brain
50	chr9:96860600-96871000	Weak transcription	Right Ventricle	heart

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