Variant report

Variant	rs9894823
Chromosome Location	chr17:38772965-38772966
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38771673..38774769-chr17:38774806..38776457,3	K562	blood:
2	chr17:38770739..38772968-chr17:38952202..38954281,2	MCF-7	breast:
3	chr17:38716724..38718551-chr17:38772418..38774994,2	MCF-7	breast:
4	chr17:38763229..38767526-chr17:38771780..38775135,4	MCF-7	breast:
5	chr17:38732692..38734383-chr17:38772868..38775729,2	MCF-7	breast:
6	chr17:38588496..38590793-chr17:38771686..38774374,2	MCF-7	breast:
7	chr17:38770013..38773292-chr17:38776635..38779762,4	MCF-7	breast:
8	chr17:38481166..38483354-chr17:38771299..38774149,2	MCF-7	breast:
9	chr17:38688685..38691278-chr17:38771780..38774213,2	MCF-7	breast:
10	chr17:38772124..38774636-chr17:38774789..38776541,3	MCF-7	breast:
11	chr17:38707503..38711120-chr17:38769935..38775644,8	MCF-7	breast:
12	chr17:38705642..38709928-chr17:38772338..38775854,5	MCF-7	breast:
13	chr17:38733163..38735894-chr17:38771819..38775610,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000126353	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11654834	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11659024	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1474454	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs16966093	0.86[ASN][1000 genomes]
rs2429548	0.82[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap]
rs2429551	0.84[JPT][hapmap]
rs2462957	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2462960	0.82[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap]
rs2462961	0.86[JPT][hapmap]
rs2469825	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs55664118	0.92[ASN][1000 genomes]
rs6503545	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6503546	0.86[ASN][1000 genomes]
rs67138687	0.86[ASN][1000 genomes]
rs7218478	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7224919	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8066541	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8074179	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8074758	0.86[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap]
rs874889	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs887376	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9303294	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs9630727	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9630729	0.86[ASN][1000 genomes]
rs9902509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv574994	chr17:38719799-38824636	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv2758454	chr17:38748300-38850104	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2758689	chr17:38748300-38850104	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv431626	chr17:38770965-38999722	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9894823	KRT24	cis	Esophagus Mucosa	GTEx
rs9894823	SMARCE1	cis	multi-tissue	Pritchard
rs9894823	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL
rs9894823	CCR7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38763400-38775600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr17:38769600-38784200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr17:38770000-38773400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr17:38770000-38773600	Enhancers	Primary T cells fromperipheralblood	blood
5	chr17:38770400-38773600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr17:38770400-38774000	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr17:38770600-38774000	Weak transcription	Right Atrium	heart
8	chr17:38770800-38773000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr17:38770800-38776200	Enhancers	Placenta	Placenta
10	chr17:38771000-38775200	Weak transcription	Fetal Kidney	kidney
11	chr17:38771400-38774000	Weak transcription	Lung	lung
12	chr17:38771400-38775200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr17:38771600-38774200	Enhancers	Primary B cells from cord blood	blood
14	chr17:38771600-38774400	Enhancers	Primary B cells from peripheral blood	blood
15	chr17:38771800-38773200	Enhancers	Primary T cells from cord blood	blood
16	chr17:38771800-38773200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr17:38771800-38773600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr17:38772000-38773600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr17:38772000-38774000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr17:38772000-38776400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr17:38772000-38784600	Weak transcription	Gastric	stomach
22	chr17:38772000-38785000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr17:38772200-38773400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr17:38772200-38774000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr17:38772200-38774200	Enhancers	Esophagus	oesophagus
26	chr17:38772200-38774200	Weak transcription	Fetal Intestine Large	intestine
27	chr17:38772200-38775000	Weak transcription	Liver	Liver
28	chr17:38772200-38775800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr17:38772200-38776200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr17:38772400-38774200	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr17:38772400-38774400	Enhancers	GM12878-XiMat	blood
32	chr17:38772400-38775400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr17:38772400-38775400	Weak transcription	A549	lung
34	chr17:38772400-38776200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr17:38772400-38778800	Weak transcription	Spleen	Spleen
36	chr17:38772400-38783600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr17:38772600-38773800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr17:38772600-38773800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr17:38772600-38774000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr17:38772600-38774000	Bivalent Enhancer	HepG2	liver
41	chr17:38772600-38774200	Weak transcription	Fetal Lung	lung
42	chr17:38772600-38774800	Enhancers	Fetal Stomach	stomach
43	chr17:38772600-38775400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr17:38772600-38775600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr17:38772600-38775800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr17:38772600-38785000	Weak transcription	Ovary	ovary
47	chr17:38772800-38773000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr17:38772800-38773800	Weak transcription	Fetal Intestine Small	intestine
49	chr17:38772800-38774200	Enhancers	Colonic Mucosa	Colon
50	chr17:38772800-38775400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links