Variant report

Variant	rs1560569
Chromosome Location	chr11:8939887-8939888
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:8936222..8938105-chr11:8938810..8940330,2	MCF-7	breast:
2	chr11:8702949..8705431-chr11:8939246..8941790,2	K562	blood:
3	chr11:8931316..8934225-chr11:8937249..8940014,3	K562	blood:
4	chr11:8932894..8935848-chr11:8939704..8942877,3	MCF-7	breast:
5	chr11:8714148..8716877-chr11:8938589..8940698,2	K562	blood:

Variant related genes	Relation type
ENSG00000166441	Chromatin interaction
ENSG00000166444	Chromatin interaction
ENSG00000254665	Chromatin interaction
ENSG00000166452	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10743093	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10743095	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10743096	0.81[ASN][1000 genomes]
rs10769967	0.93[CEU][hapmap]
rs10769968	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10769970	0.93[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10769971	0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10769973	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10769979	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs10769980	0.84[EUR][1000 genomes]
rs10769981	0.81[EUR][1000 genomes]
rs10840130	0.84[CEU][hapmap]
rs10840134	0.92[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap]
rs10840141	0.93[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10840142	0.93[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10840147	0.89[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10840148	0.93[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10840157	0.87[EUR][1000 genomes]
rs10840160	0.81[TSI][hapmap]
rs11042078	0.89[CEU][hapmap];0.82[MEX][hapmap];0.86[YRI][hapmap]
rs11042102	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11042103	0.93[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11042125	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11042149	0.89[CEU][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap]
rs11042151	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs11042152	0.85[EUR][1000 genomes]
rs11042154	1.00[CEU][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs1109305	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1123936	0.93[CEU][hapmap];0.90[GIH][hapmap];0.87[MEX][hapmap]
rs11603841	0.88[CEU][hapmap]
rs1529641	0.91[CEU][hapmap]
rs1569408	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1883098	0.86[EUR][1000 genomes]
rs1980428	0.93[CEU][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap]
rs1980429	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs1984791	0.81[JPT][hapmap]
rs1988708	0.83[EUR][1000 genomes]
rs1988709	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2012696	0.87[EUR][1000 genomes]
rs2016942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2568043	0.92[CEU][hapmap]
rs2568045	0.93[CEU][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap]
rs2568054	0.83[EUR][1000 genomes]
rs2568059	0.85[EUR][1000 genomes]
rs2568061	0.93[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs2568062	0.86[EUR][1000 genomes]
rs2568065	0.93[CEU][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs2568090	0.93[CEU][hapmap];0.82[MEX][hapmap]
rs2653567	0.86[EUR][1000 genomes]
rs2653570	0.89[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap]
rs2653593	0.84[EUR][1000 genomes]
rs2653605	0.93[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap]
rs2653616	0.85[EUR][1000 genomes]
rs2742471	0.85[EUR][1000 genomes]
rs2742474	0.84[EUR][1000 genomes]
rs2742480	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs2742537	0.83[CEU][hapmap]
rs2742540	0.85[CEU][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs2742545	0.85[CEU][hapmap]
rs2742550	0.84[EUR][1000 genomes]
rs2742552	0.85[CEU][hapmap];0.95[MEX][hapmap]
rs34842234	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4909952	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4910062	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs4910119	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4910156	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4910157	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910158	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910200	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4910442	0.91[CEU][hapmap]
rs4929922	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6486060	0.92[CEU][hapmap]
rs7119939	0.92[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7123429	0.93[CEU][hapmap]
rs7123861	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7479407	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs7484180	0.86[EUR][1000 genomes]
rs7925728	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs7930026	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes]
rs7937298	0.93[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7945705	0.93[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription 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 target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1560569	AKIP1	cis	Thyroid	GTEx
rs1560569	RRP8	cis	parietal	SCAN
rs1560569	OR51Q1	cis	parietal	SCAN
rs1560569	MMP26	cis	cerebellum	SCAN
rs1560569	C11orf17	cis	lymphoblastoid	seeQTL
rs1560569	NRIP3	cis	parietal	SCAN
rs1560569	WEE1	cis	parietal	SCAN
rs1560569	TMEM9B-AS1	cis	lung	GTEx
rs1560569	TMEM9B	cis	parietal	SCAN
rs1560569	CYB5R2	cis	parietal	SCAN
rs1560569	C11orf17	cis	multi-tissue	Pritchard
rs1560569	TRIM22	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8933400-8947800	Weak transcription	Small Intestine	intestine
2	chr11:8933600-8944000	Weak transcription	Pancreas	Pancrea
3	chr11:8934000-8941800	Weak transcription	Colonic Mucosa	Colon
4	chr11:8934000-8952200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:8934200-8941600	Weak transcription	Esophagus	oesophagus
6	chr11:8934200-8948800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:8935000-8940400	Genic enhancers	Fetal Muscle Leg	muscle
8	chr11:8935800-8940000	Weak transcription	Gastric	stomach
9	chr11:8936000-8942800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr11:8936200-8945800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr11:8936400-8941800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr11:8936400-8946000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr11:8936400-8946800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr11:8936400-8951200	Weak transcription	Right Atrium	heart
15	chr11:8936600-8940600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr11:8936600-8940800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr11:8936600-8941400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr11:8936600-8941600	Weak transcription	Ovary	ovary
19	chr11:8936600-8945000	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr11:8936600-8945800	Weak transcription	Stomach Mucosa	stomach
21	chr11:8936600-8946600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr11:8936600-8948600	Strong transcription	Fetal Thymus	thymus
23	chr11:8936600-8949000	Strong transcription	Fetal Stomach	stomach
24	chr11:8936600-8954000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr11:8936800-8940000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr11:8936800-8942200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr11:8936800-8947000	Strong transcription	Dnd41	blood
28	chr11:8936800-8947600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr11:8937000-8947600	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr11:8937000-8948200	Strong transcription	Fetal Brain Female	brain
31	chr11:8937200-8945000	Strong transcription	Brain Angular Gyrus	brain
32	chr11:8937200-8947400	Strong transcription	Thymus	Thymus
33	chr11:8937600-8944800	Strong transcription	Hela-S3	cervix
34	chr11:8937800-8940200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr11:8937800-8940800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr11:8937800-8947400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr11:8938000-8940200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:8938000-8940200	Enhancers	Rectal Smooth Muscle	rectum
39	chr11:8938000-8941200	Enhancers	Placenta Amnion	Placenta Amnion
40	chr11:8938000-8941200	Strong transcription	K562	blood
41	chr11:8938000-8943000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr11:8938000-8943200	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr11:8938000-8944200	Strong transcription	HUVEC	blood vessel
44	chr11:8938000-8944600	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr11:8938000-8944800	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr11:8938000-8944800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr11:8938000-8944800	Strong transcription	Fetal Intestine Large	intestine
48	chr11:8938000-8945000	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr11:8938000-8945000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr11:8938000-8945800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links