Variant report

Variant	rs11090564
Chromosome Location	chr22:29704125-29704126
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr22:29704109-29705465	ECC-1	luminal epithelium:	n/a	chr22:29704846-29704856 chr22:29705377-29705387
2	RCOR1	chr22:29701922-29704280	IMR90	lung:	n/a	n/a
3	EP300	chr22:29704049-29705881	ECC-1	luminal epithelium:	n/a	n/a
4	MAZ	chr22:29701830-29704170	IMR90	lung:	n/a	chr22:29702885-29702895
5	MAX	chr22:29703959-29705178	NB4	blood:	n/a	chr22:29704846-29704856
6	POLR2A	chr22:29704061-29704159	K562	blood:	n/a	n/a
7	POLR2A	chr22:29703776-29705696	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:29702549..29705407-chr22:29734900..29738437,3	MCF-7	breast:
2	chr22:29660929..29666447-chr22:29700529..29705135,9	K562	blood:
3	chr22:29700857..29704420-chr22:29708764..29712339,6	MCF-7	breast:
4	chr22:29703109..29706869-chr22:29711325..29716000,5	K562	blood:
5	chr22:29701804..29704290-chr22:29781998..29785634,5	MCF-7	breast:
6	chr22:29663358..29665751-chr22:29702504..29704805,4	MCF-7	breast:
7	chr22:29702481..29704174-chr22:29874105..29876353,2	K562	blood:

Variant related genes	Relation type
GAS2L1	TF binding region
ENSG00000100263	Chromatin interaction
ENSG00000273216	Chromatin interaction
ENSG00000182944	Chromatin interaction
ENSG00000225465	Chromatin interaction
ENSG00000100285	Chromatin interaction
ENSG00000100276	Chromatin interaction
ENSG00000100280	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs131180	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs131182	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs131189	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs140062	0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs140063	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs140066	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs174759	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs174761	0.81[ASW][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs174762	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs174764	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs174765	0.92[ASN][1000 genomes]
rs174766	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs174767	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs174769	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs174770	0.93[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs174771	0.89[ASN][1000 genomes]
rs174775	0.83[CHD][hapmap]
rs2071578	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072051	0.93[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs2267132	0.83[JPT][hapmap]
rs2267133	0.87[ASW][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap]
rs2283849	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2283850	0.93[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2301290	0.94[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2301291	0.80[JPT][hapmap]
rs2301585	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2519486	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2857462	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2857466	0.89[JPT][hapmap]
rs28755	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3788410	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3788411	0.88[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.80[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4820803	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs4820804	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5752903	0.93[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs5763138	0.94[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs5763139	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5763178	0.89[ASN][1000 genomes]
rs6006090	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6006098	0.87[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs715494	0.93[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs737883	0.80[JPT][hapmap]
rs762817	0.82[ASN][1000 genomes]
rs879580	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs909798	0.84[JPT][hapmap]
rs9537	0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs98069	0.88[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv829154	chr22:29617485-29724001	Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription 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	24 gene(s)	inside rSNPs	diseases
3	nsv834171	chr22:29626402-29829844	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv829155	chr22:29664396-29724001	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription 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	21 gene(s)	inside rSNPs	diseases
5	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv914959	chr22:29696438-29712874	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv914960	chr22:29696438-29714069	Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11090564	RNF185	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29702000-29704400	Flanking Active TSS	Colonic Mucosa	Colon
2	chr22:29702000-29705600	Active TSS	Fetal Brain Female	brain
3	chr22:29702000-29707800	Enhancers	Fetal Heart	heart
4	chr22:29702200-29704200	Active TSS	A549	lung
5	chr22:29702200-29704600	Active TSS	Brain Anterior Caudate	brain
6	chr22:29702800-29706400	Weak transcription	GM12878-XiMat	blood
7	chr22:29703000-29704800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr22:29703000-29706400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr22:29703200-29704400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
10	chr22:29703200-29705000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr22:29703200-29707600	Enhancers	Fetal Brain Male	brain
12	chr22:29703400-29704200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr22:29703400-29704200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
14	chr22:29703400-29704400	Flanking Active TSS	Brain Cingulate Gyrus	brain
15	chr22:29703400-29704400	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr22:29703400-29704400	Flanking Active TSS	K562	blood
17	chr22:29703400-29705000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr22:29703400-29705600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr22:29703400-29705600	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr22:29703400-29705600	Flanking Active TSS	Osteobl	bone
21	chr22:29703400-29705800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr22:29703400-29705800	Flanking Active TSS	NH-A	brain
23	chr22:29703600-29704200	Flanking Active TSS	HUVEC	blood vessel
24	chr22:29703600-29704400	Flanking Active TSS	Brain Angular Gyrus	brain
25	chr22:29703600-29704400	Flanking Active TSS	Lung	lung
26	chr22:29703600-29704600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr22:29703600-29704600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr22:29703600-29704600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr22:29703600-29704600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr22:29703600-29704600	Flanking Active TSS	Brain Hippocampus Middle	brain
31	chr22:29703600-29705200	Flanking Active TSS	Esophagus	oesophagus
32	chr22:29703600-29705400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr22:29703600-29705400	Flanking Active TSS	NHEK	skin
34	chr22:29703600-29705600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
35	chr22:29703600-29705600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr22:29703600-29705600	Flanking Active TSS	HMEC	breast
37	chr22:29703600-29705800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr22:29703600-29705800	Flanking Active TSS	Colon Smooth Muscle	Colon
39	chr22:29703600-29705800	Enhancers	Placenta Amnion	Placenta Amnion
40	chr22:29703600-29705800	Flanking Active TSS	Rectal Smooth Muscle	rectum
41	chr22:29703600-29706000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr22:29703600-29706000	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr22:29703600-29706000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr22:29703600-29706000	Flanking Active TSS	Hela-S3	cervix
45	chr22:29703600-29706800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr22:29703600-29707600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr22:29703600-29707800	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr22:29703600-29708000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr22:29703800-29704200	Enhancers	Pancreas	Pancrea
50	chr22:29703800-29704200	Enhancers	Spleen	Spleen

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