Variant report

Variant	rs585522
Chromosome Location	chr12:123550813-123550814
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123547288..123551146-chr12:123559107..123563202,4	MCF-7	breast:
2	chr12:123549316..123551097-chr12:123632529..123635148,2	K562	blood:
3	chr12:123547555..123551371-chr12:123552619..123557163,4	MCF-7	breast:
4	chr12:123550533..123552152-chr12:123560273..123563222,2	MCF-7	breast:
5	chr12:123544559..123546655-chr12:123548613..123551754,3	K562	blood:

Variant related genes	Relation type
ENSG00000090975	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1051431	0.89[TSI][hapmap]
rs10773921	0.80[GIH][hapmap]
rs10848428	0.80[GIH][hapmap]
rs11057192	0.88[TSI][hapmap]
rs1106240	0.86[TSI][hapmap]
rs1106241	0.89[TSI][hapmap]
rs11608811	0.80[GIH][hapmap]
rs1260294	0.84[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs12811109	0.82[EUR][1000 genomes]
rs12820906	0.94[CHB][hapmap]
rs12828755	0.81[EUR][1000 genomes]
rs1402274	0.89[TSI][hapmap]
rs1463877	0.84[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs1569068	0.89[TSI][hapmap]
rs1617156	1.00[ASW][hapmap];0.84[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1716157	0.89[TSI][hapmap]
rs1716160	0.88[TSI][hapmap]
rs1716164	0.89[TSI][hapmap]
rs1716165	0.89[TSI][hapmap]
rs1716167	0.89[TSI][hapmap]
rs1716168	0.89[TSI][hapmap]
rs1716170	0.86[TSI][hapmap]
rs1716171	0.86[TSI][hapmap]
rs1727294	0.85[ASN][1000 genomes]
rs1727307	0.80[GIH][hapmap];0.86[MEX][hapmap];0.85[YRI][hapmap]
rs1727309	0.83[TSI][hapmap]
rs1727313	0.86[TSI][hapmap]
rs1727315	0.89[TSI][hapmap]
rs1727323	0.89[TSI][hapmap]
rs1790094	0.80[GIH][hapmap]
rs1790095	0.89[TSI][hapmap]
rs1790098	0.89[TSI][hapmap]
rs1790106	0.80[GIH][hapmap]
rs1790108	0.89[TSI][hapmap]
rs1790116	0.89[TSI][hapmap]
rs1790120	0.81[ASN][1000 genomes]
rs1790121	0.80[GIH][hapmap]
rs1790123	0.86[TSI][hapmap]
rs1790131	0.89[TSI][hapmap]
rs1879380	0.80[TSI][hapmap]
rs1969354	0.83[TSI][hapmap]
rs2270789	0.94[CHB][hapmap];0.84[CHD][hapmap];0.87[ASN][1000 genomes]
rs2337934	0.86[TSI][hapmap]
rs2510885	0.85[ASN][1000 genomes]
rs2682434	0.89[TSI][hapmap]
rs2695478	0.86[TSI][hapmap]
rs4148863	0.80[GIH][hapmap]
rs4759371	0.86[TSI][hapmap]
rs4759415	0.86[TSI][hapmap]
rs520088	1.00[ASW][hapmap];0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs641760	1.00[ASW][hapmap];0.84[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.92[TSI][hapmap]
rs655293	1.00[ASW][hapmap];0.84[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.88[LWK][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7132277	0.81[TSI][hapmap]
rs71444568	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7296418	0.85[MEX][hapmap];0.87[YRI][hapmap]
rs7299943	0.93[ASW][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7975763	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs883263	1.00[ASW][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.85[LWK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.85[EUR][1000 genomes]
rs883563	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs937564	1.00[ASW][hapmap];0.84[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];0.85[EUR][1000 genomes]
rs940904	0.93[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.82[TSI][hapmap];0.92[YRI][hapmap];0.82[ASN][1000 genomes]
rs949143	0.80[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS 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 miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' 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	37 gene(s)	inside rSNPs	diseases
5	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
6	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv560494	chr12:123478378-123560731	Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs585522	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs585522	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs585522	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs585522	PITPNM2	cis	cerebellum	SCAN
rs585522	MPHOSPH9	cis	Esophagus Muscularis	GTEx
rs585522	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs585522	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs585522	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs585522	ANAPC5	cis	parietal	SCAN
rs585522	SETD8	Cis_1M	lymphoblastoid	RTeQTL
rs585522	CDK2AP1	cis	lymphoblastoid	seeQTL
rs585522	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs585522	TMEM120B	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123537800-123551200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:123539600-123552600	Enhancers	Right Ventricle	heart
3	chr12:123541800-123551200	Enhancers	Fetal Muscle Leg	muscle
4	chr12:123542200-123551200	Enhancers	Fetal Muscle Trunk	muscle
5	chr12:123542800-123563800	Enhancers	Left Ventricle	heart
6	chr12:123543000-123551400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:123543200-123552600	Enhancers	Lung	lung
8	chr12:123543400-123551000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr12:123543400-123551200	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr12:123543400-123551400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:123543400-123552600	Enhancers	Right Atrium	heart
12	chr12:123543600-123552600	Enhancers	Brain Hippocampus Middle	brain
13	chr12:123543800-123559000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:123544000-123552800	Enhancers	Psoas Muscle	Psoas
15	chr12:123544000-123559000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:123544600-123554800	Weak transcription	Fetal Lung	lung
17	chr12:123545000-123552200	Enhancers	Primary T cells from cord blood	blood
18	chr12:123545400-123551000	Enhancers	Pancreas	Pancrea
19	chr12:123545800-123551000	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr12:123546000-123552600	Transcr. at gene 5' and 3'	Thymus	Thymus
21	chr12:123546200-123551000	Enhancers	Primary B cells from peripheral blood	blood
22	chr12:123546400-123551000	Enhancers	Brain Angular Gyrus	brain
23	chr12:123546400-123562400	Enhancers	Liver	Liver
24	chr12:123546600-123551000	Enhancers	Brain Substantia Nigra	brain
25	chr12:123546600-123551000	Enhancers	Fetal Brain Male	brain
26	chr12:123546600-123551200	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr12:123546600-123552400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr12:123546800-123551000	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr12:123546800-123551200	Enhancers	Esophagus	oesophagus
30	chr12:123547000-123551000	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr12:123547000-123551000	Enhancers	Duodenum Mucosa	Duodenum
32	chr12:123547200-123551000	Enhancers	Brain Cingulate Gyrus	brain
33	chr12:123547200-123551400	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr12:123547400-123551000	Enhancers	Ovary	ovary
35	chr12:123547400-123551200	Enhancers	Colonic Mucosa	Colon
36	chr12:123547400-123551600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:123547800-123552600	Enhancers	Primary T cells fromperipheralblood	blood
38	chr12:123548000-123551000	Enhancers	HSMM	muscle
39	chr12:123548000-123554600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:123548000-123555000	Weak transcription	HUVEC	blood vessel
41	chr12:123548200-123551800	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr12:123548200-123552000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:123548600-123551400	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr12:123549000-123551400	Enhancers	Colon Smooth Muscle	Colon
45	chr12:123549000-123554000	Weak transcription	HMEC	breast
46	chr12:123549000-123554600	Weak transcription	Small Intestine	intestine
47	chr12:123549200-123553600	Weak transcription	Fetal Intestine Large	intestine
48	chr12:123549400-123551400	Genic enhancers	Fetal Stomach	stomach
49	chr12:123549400-123554400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:123549400-123555000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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