Variant report

Variant	rs2281212
Chromosome Location	chr20:25465589-25465590
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25464881..25466399-chr20:25468189..25469773,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11696666	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11698953	0.85[EUR][1000 genomes]
rs11698992	0.85[EUR][1000 genomes]
rs11699872	0.93[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11700213	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11700297	0.83[EUR][1000 genomes]
rs11700338	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.83[MKK][hapmap]
rs12480853	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs12481037	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs12481409	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12625157	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs12625748	0.85[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap]
rs12625991	0.81[EUR][1000 genomes]
rs1888037	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs2050097	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2072976	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274890	0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs3736720	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3764694	1.00[ASW][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4815438	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs6037190	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs6050690	0.87[CHB][hapmap]
rs6107050	0.84[ASN][1000 genomes]
rs6115202	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs6115227	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs6115241	0.83[CHB][hapmap]
rs66807280	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs68053392	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73109499	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73597807	0.83[ASN][1000 genomes]
rs73597820	0.82[EUR][1000 genomes]
rs9305141	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS 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 target site	53 gene(s)	inside rSNPs	diseases
4	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
9	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
11	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
12	nsv482647	chr20:25308912-25481982	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
13	nsv1056997	chr20:25316663-25492339	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
14	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
15	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
16	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
17	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
18	nsv912828	chr20:25433015-25595175	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
19	nsv1062452	chr20:25438025-25590278	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
20	nsv1066066	chr20:25439367-25588016	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
21	nsv544224	chr20:25439367-25588016	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
22	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
23	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
24	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2281212	HDHD4	cis	multi-tissue	Pritchard
rs2281212	C20orf22	cis	multi-tissue	Pritchard
rs2281212	ABHD12	cis	lymphoblastoid	seeQTL
rs2281212	ABHD12	cis	cerebellum	SCAN
rs2281212	KIAA0980	cis	multi-tissue	Pritchard
rs2281212	GINS1	cis	parietal	SCAN
rs2281212	ABHD12	cis	Temporal Cortex	GTEx
rs2281212	PYGB	cis	cerebellum	SCAN
rs2281212	NINL	cis	cerebellum	SCAN
rs2281212	NINL	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25427200-25488200	Weak transcription	Stomach Mucosa	stomach
2	chr20:25430200-25484400	Strong transcription	Fetal Stomach	stomach
3	chr20:25431800-25484200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr20:25435800-25465600	Weak transcription	NH-A	brain
5	chr20:25438600-25466200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr20:25438800-25472600	Strong transcription	HepG2	liver
7	chr20:25440600-25466600	Weak transcription	Left Ventricle	heart
8	chr20:25446000-25466600	Weak transcription	NHDF-Ad	bronchial
9	chr20:25446000-25489600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr20:25446400-25488200	Weak transcription	Right Atrium	heart
11	chr20:25447000-25477600	Strong transcription	Fetal Muscle Leg	muscle
12	chr20:25448200-25490600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr20:25448600-25484200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr20:25448800-25480800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr20:25451200-25474000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr20:25451400-25468400	Weak transcription	Osteobl	bone
17	chr20:25451400-25488800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr20:25451600-25470000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr20:25451800-25468000	Weak transcription	HSMMtube	muscle
20	chr20:25453400-25494400	Strong transcription	Brain Germinal Matrix	brain
21	chr20:25453600-25467200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr20:25456200-25466200	Strong transcription	Fetal Intestine Small	intestine
23	chr20:25456400-25470800	Strong transcription	Fetal Lung	lung
24	chr20:25456400-25472600	Strong transcription	Fetal Intestine Large	intestine
25	chr20:25456600-25469600	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr20:25457000-25471600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr20:25457600-25474000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr20:25457800-25489000	Weak transcription	Placenta	Placenta
29	chr20:25459800-25489800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr20:25460200-25469600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr20:25461200-25468000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr20:25461600-25465600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr20:25461600-25466800	Weak transcription	Fetal Heart	heart
34	chr20:25461600-25468200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr20:25461800-25469600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr20:25462600-25468600	Weak transcription	Brain Hippocampus Middle	brain
37	chr20:25462600-25469400	Weak transcription	NHLF	lung
38	chr20:25462600-25469600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr20:25462800-25466600	Weak transcription	Aorta	Aorta
40	chr20:25462800-25466600	Weak transcription	Ovary	ovary
41	chr20:25462800-25467200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr20:25462800-25467800	Weak transcription	Colon Smooth Muscle	Colon
43	chr20:25462800-25468000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr20:25462800-25468400	Weak transcription	Lung	lung
45	chr20:25462800-25468600	Weak transcription	Gastric	stomach
46	chr20:25462800-25468800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr20:25462800-25469600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr20:25462800-25471400	Weak transcription	Brain Anterior Caudate	brain
49	chr20:25462800-25474800	Weak transcription	Right Ventricle	heart
50	chr20:25462800-25488200	Weak transcription	Colonic Mucosa	Colon

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