Variant report

Variant	rs569602
Chromosome Location	chr11:64514506-64514507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64514464..64517911-chr11:64519413..64523331,4	MCF-7	breast:
2	chr11:64507790..64516181-chr11:64524582..64537783,30	K562	blood:
3	chr11:64510354..64515027-chr11:64543156..64548358,11	K562	blood:
4	chr11:64513308..64515346-chr11:64576654..64578254,2	K562	blood:

Variant related genes	Relation type
ENSG00000068976	Chromatin interaction
ENSG00000168066	Chromatin interaction
ENSG00000269038	Chromatin interaction
ENSG00000133895	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10897524	0.86[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10897525	0.88[MEX][hapmap];0.81[AMR][1000 genomes]
rs11231859	0.92[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11231869	0.88[MEX][hapmap]
rs1143937	0.88[MEX][hapmap]
rs1207113	0.91[ASN][1000 genomes]
rs1207181	0.91[ASN][1000 genomes]
rs12223914	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417551	0.80[EUR][1000 genomes]
rs1633462	0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17146121	0.81[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs2003293	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2073797	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2230414	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2267918	0.92[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs2284301	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2375335	0.85[EUR][1000 genomes]
rs2959652	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3741398	0.94[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes]
rs3809076	0.92[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs474707	0.85[CHB][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs476037	0.81[GIH][hapmap];1.00[MEX][hapmap]
rs477549	0.86[CHB][hapmap];0.81[CHD][hapmap];0.89[MEX][hapmap];0.85[EUR][1000 genomes]
rs483962	0.86[CHB][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs487105	0.81[CHB][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs489192	0.90[CHB][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.80[ASN][1000 genomes]
rs490980	0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs494128	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs496914	0.92[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs523200	0.86[CHB][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes]
rs532747	0.84[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs547066	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs555974	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580374	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58483071	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs589691	1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs593394	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs606458	0.81[CHB][hapmap];0.84[MEX][hapmap]
rs620006	0.83[EUR][1000 genomes]
rs624975	0.88[MEX][hapmap]
rs625172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs630966	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs633923	0.83[EUR][1000 genomes]
rs637332	0.86[CHB][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs667237	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs669976	0.88[MEX][hapmap]
rs673224	0.82[EUR][1000 genomes]
rs674297	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs675254	1.00[CEU][hapmap]
rs677298	0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs680273	0.86[CHB][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.80[EUR][1000 genomes]
rs684720	0.82[AMR][1000 genomes]
rs686171	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs693235	0.92[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap]
rs72643567	0.83[EUR][1000 genomes]
rs72643568	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7938455	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7939965	0.81[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468596	chr11:64334114-64527080	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv555195	chr11:64334114-64527080	Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv897694	chr11:64334114-64584959	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv818842	chr11:64345448-64546391	Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
6	nsv555196	chr11:64357072-64559898	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
7	nsv897695	chr11:64357072-64701030	Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
8	nsv1051350	chr11:64372906-64533632	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv555198	chr11:64373899-64573589	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	esv1804443	chr11:64386453-64534785	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv897697	chr11:64447420-64584959	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
12	nsv897698	chr11:64447420-64621573	Active TSS Bivalent Enhancer Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
13	nsv897699	chr11:64447420-64638041	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
14	nsv897700	chr11:64447420-64701030	Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1071 gene(s)	inside rSNPs	diseases
15	nsv555202	chr11:64477050-64573589	Strong transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
16	nsv468597	chr11:64477050-64584959	Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
17	nsv468598	chr11:64477050-64584959	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
18	nsv555203	chr11:64477050-64584959	Strong transcription Genic enhancers Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
19	nsv1049744	chr11:64486615-64630149	Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
20	nsv832189	chr11:64487183-64620199	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
21	nsv897701	chr11:64501991-64520569	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs569602	SF1	cis	multi-tissue	Pritchard
rs569602	PYGM	cis	cerebellum	SCAN
rs569602	MALAT1	cis	parietal	SCAN
rs569602	ANKRD13D	cis	parietal	SCAN
rs569602	SF1	cis	lymphoblastoid	seeQTL
rs569602	B3GNT1	cis	cerebellum	SCAN
rs569602	PYGM	cis	parietal	SCAN
rs569602	SF1	Cis_1M	lymphoblastoid	RTeQTL
rs569602	CABP2	cis	parietal	SCAN
rs569602	TMEM138	cis	cerebellum	SCAN
rs569602	EHD1	cis	cerebellum	SCAN
rs569602	ACY3	cis	parietal	SCAN
rs569602	TMEM138	cis	parietal	SCAN
rs569602	LRRN4CL	cis	cerebellum	SCAN
rs569602	POLA2	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64512800-64526400	Weak transcription	Ovary	ovary
2	chr11:64513400-64515600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr11:64513400-64517600	Weak transcription	Colon Smooth Muscle	Colon
4	chr11:64513400-64529800	Weak transcription	Liver	Liver
5	chr11:64513400-64530000	Weak transcription	Aorta	Aorta
6	chr11:64513600-64514800	Enhancers	Primary T cells from cord blood	blood
7	chr11:64513600-64514800	Enhancers	Fetal Muscle Trunk	muscle
8	chr11:64513600-64514800	Enhancers	Fetal Muscle Leg	muscle
9	chr11:64513600-64514800	Bivalent Enhancer	Placenta	Placenta
10	chr11:64513600-64515600	Weak transcription	NHLF	lung
11	chr11:64513600-64516000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr11:64513600-64518800	Weak transcription	Brain Substantia Nigra	brain
13	chr11:64513600-64518800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr11:64513600-64518800	Weak transcription	Left Ventricle	heart
15	chr11:64513600-64522200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr11:64513600-64525600	Weak transcription	Psoas Muscle	Psoas
17	chr11:64513600-64526200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr11:64513600-64526200	Weak transcription	Esophagus	oesophagus
19	chr11:64513800-64514600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr11:64513800-64514600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr11:64513800-64514800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr11:64513800-64515000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
23	chr11:64513800-64515200	Enhancers	Primary hematopoietic stem cells	blood
24	chr11:64513800-64515200	Enhancers	Fetal Thymus	thymus
25	chr11:64513800-64515600	Weak transcription	Fetal Brain Male	brain
26	chr11:64513800-64515800	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr11:64513800-64517600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr11:64513800-64517800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr11:64513800-64519200	Weak transcription	Brain Anterior Caudate	brain
30	chr11:64513800-64526400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr11:64513800-64526800	Weak transcription	Brain Hippocampus Middle	brain
32	chr11:64513800-64526800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr11:64514000-64515000	Enhancers	Primary B cells from peripheral blood	blood
34	chr11:64514000-64515000	Enhancers	Primary T cells fromperipheralblood	blood
35	chr11:64514000-64515200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr11:64514000-64517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr11:64514000-64518800	Weak transcription	Lung	lung
38	chr11:64514000-64518800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr11:64514000-64521000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr11:64514000-64526800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr11:64514000-64529800	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr11:64514200-64514600	Enhancers	Placenta Amnion	Placenta Amnion
43	chr11:64514200-64514600	Enhancers	Dnd41	blood
44	chr11:64514200-64514800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr11:64514200-64515200	Enhancers	Stomach Smooth Muscle	stomach
46	chr11:64514200-64515600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr11:64514200-64515800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr11:64514200-64516000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
49	chr11:64514200-64517600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr11:64514200-64517600	Weak transcription	Fetal Stomach	stomach

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