Variant report

Variant	rs12311043
Chromosome Location	chr12:123440612-123440613
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr12:123440506-123441107	MCF-7	breast:	n/a	n/a
2	REST	chr12:123440611-123440942	Hela-S3	cervix:	n/a	n/a
3	REST	chr12:123440586-123440906	SK-N-SH	brain:	n/a	n/a
4	REST	chr12:123440467-123441114	ECC-1	luminal epithelium:	n/a	n/a
5	REST	chr12:123440612-123440918	K562	blood:	n/a	n/a
6	REST	chr12:123440535-123441169	ECC-1	luminal epithelium:	n/a	n/a
7	REST	chr12:123440547-123440988	HCT-116	colon:	n/a	n/a
8	REST	chr12:123440583-123440926	A549	lung:	n/a	n/a
9	REST	chr12:123440430-123441078	PANC-1	pancreas:	n/a	n/a
10	REST	chr12:123440457-123441130	HL-60	blood:	n/a	n/a
11	TEAD4	chr12:123440540-123441033	A549	lung:	n/a	n/a
12	REST	chr12:123440508-123441034	PFSK-1	brain:	n/a	n/a
13	REST	chr12:123440589-123440957	H1-hESC	embryonic stem cell:	n/a	n/a
14	REST	chr12:123440529-123441076	PANC-1	pancreas:	n/a	n/a
15	REST	chr12:123440612-123440959	H1-hESC	embryonic stem cell:	n/a	n/a
16	REST	chr12:123440558-123441027	PFSK-1	brain:	n/a	n/a
17	REST	chr12:123440497-123440953	U87	brain:	n/a	n/a
18	REST	chr12:123440472-123441027	GM12878	blood:	n/a	n/a
19	REST	chr12:123440528-123440991	HL-60	blood:	n/a	n/a
20	REST	chr12:123440532-123440917	Hela-S3	cervix:	n/a	n/a
21	REST	chr12:123440573-123441011	PANC-1	pancreas:	n/a	n/a
22	REST	chr12:123440545-123440915	U87	brain:	n/a	n/a
23	REST	chr12:123440454-123441044	A549	lung:	n/a	n/a
24	REST	chr12:123440585-123441046	MCF-7	breast:	n/a	n/a
25	REST	chr12:123440536-123440898	PANC-1	pancreas:	n/a	n/a
26	REST	chr12:123440567-123440993	HCT-116	colon:	n/a	n/a
27	REST	chr12:123440477-123440930	SK-N-SH	brain:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123354937..123357622-chr12:123439392..123442120,2	MCF-7	breast:
2	chr12:123348847..123350779-chr12:123438689..123440697,2	K562	blood:
3	chr12:123434699..123436305-chr12:123439447..123441545,2	K562	blood:

No data

Variant related genes	Relation type
ABCB9	TF binding region
ENSG00000256152	Chromatin interaction
ENSG00000139722	Chromatin interaction
ENSG00000150967	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10219462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1026395	1.00[JPT][hapmap]
rs1037593	1.00[JPT][hapmap]
rs10431343	1.00[CHB][hapmap]
rs10773599	1.00[JPT][hapmap]
rs10846468	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10846469	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs10846471	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs10846473	0.87[ASN][1000 genomes]
rs10847742	1.00[JPT][hapmap]
rs10847749	1.00[JPT][hapmap]
rs10847751	1.00[JPT][hapmap]
rs10847775	1.00[JPT][hapmap]
rs10847910	1.00[JPT][hapmap]
rs10848148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10848363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10848365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs10848429	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11057172	0.87[ASN][1000 genomes]
rs11060152	1.00[JPT][hapmap]
rs11060888	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11060932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11060997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11060999	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061166	0.87[ASN][1000 genomes]
rs11061601	0.87[ASN][1000 genomes]
rs11061611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs11061616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12229119	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12229884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12298355	0.87[ASN][1000 genomes]
rs12302334	1.00[CHD][hapmap]
rs12306711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12311134	0.87[ASN][1000 genomes]
rs12318594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs12366787	0.87[ASN][1000 genomes]
rs1260121	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1671684	1.00[JPT][hapmap]
rs1671687	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1696355	1.00[CHB][hapmap]
rs1798563	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1975761	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2061099	1.00[JPT][hapmap]
rs2343107	1.00[JPT][hapmap]
rs2649895	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2649900	1.00[CHB][hapmap]
rs2649903	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2656812	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34010146	0.92[AFR][1000 genomes]
rs3844369	1.00[JPT][hapmap]
rs4307760	1.00[JPT][hapmap]
rs4427600	0.83[ASW][hapmap];0.82[MKK][hapmap]
rs4759353	1.00[JPT][hapmap]
rs4759354	1.00[JPT][hapmap]
rs4759384	1.00[JPT][hapmap]
rs4759438	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs55813219	0.86[AFR][1000 genomes]
rs55951195	0.86[AFR][1000 genomes]
rs56150478	0.85[AFR][1000 genomes]
rs56288804	0.89[AFR][1000 genomes]
rs57110420	0.82[AFR][1000 genomes]
rs57310784	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57863319	0.86[AFR][1000 genomes]
rs58025094	0.92[AFR][1000 genomes]
rs58462666	0.86[AFR][1000 genomes]
rs59002329	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59081274	0.93[AFR][1000 genomes]
rs59211448	0.86[AFR][1000 genomes]
rs59379557	0.89[AFR][1000 genomes]
rs59526938	0.92[AFR][1000 genomes]
rs60888713	0.86[AFR][1000 genomes]
rs60987910	0.89[AFR][1000 genomes]
rs61061591	0.86[AFR][1000 genomes]
rs61546241	0.89[AFR][1000 genomes]
rs61592192	0.89[AFR][1000 genomes]
rs61677786	0.89[AFR][1000 genomes]
rs7138257	1.00[JPT][hapmap]
rs7295258	0.81[AFR][1000 genomes]
rs7298176	1.00[JPT][hapmap]
rs7306948	1.00[JPT][hapmap]
rs73408835	0.92[AFR][1000 genomes]
rs73408859	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73408862	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73408863	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73408890	0.94[AFR][1000 genomes]
rs73408892	0.94[AFR][1000 genomes]
rs73408893	0.93[AFR][1000 genomes]
rs73408894	0.94[AFR][1000 genomes]
rs73408899	0.92[AFR][1000 genomes]
rs73411006	0.86[AFR][1000 genomes]
rs73411009	0.86[AFR][1000 genomes]
rs73411011	0.86[AFR][1000 genomes]
rs73411014	0.81[AFR][1000 genomes]
rs73411015	0.86[AFR][1000 genomes]
rs73411018	0.86[AFR][1000 genomes]
rs73411027	0.89[AFR][1000 genomes]
rs73411033	0.89[AFR][1000 genomes]
rs73411041	0.89[AFR][1000 genomes]
rs73411043	0.89[AFR][1000 genomes]
rs7485652	1.00[JPT][hapmap]
rs752164	1.00[ASW][hapmap];0.89[LWK][hapmap];0.82[MKK][hapmap];0.94[YRI][hapmap]
rs7952760	1.00[ASW][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];0.94[YRI][hapmap]
rs7957096	0.94[YRI][hapmap]
rs7957643	1.00[JPT][hapmap]
rs7958155	1.00[JPT][hapmap]
rs7964036	1.00[ASW][hapmap];0.89[LWK][hapmap];0.82[MKK][hapmap];0.94[YRI][hapmap]
rs839354	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs897388	1.00[JPT][hapmap]
rs967281	1.00[JPT][hapmap]
rs9795629	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	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
5	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	nsv560491	chr12:123425575-123444422	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	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
11	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
12	nsv899577	chr12:123435248-123484474	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12311043	OGFOD2	cis	lymphoblastoid	seeQTL
rs12311043	ARL6IP4	cis	multi-tissue	Pritchard

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123403000-123444200	Weak transcription	Aorta	Aorta
2	chr12:123412800-123449200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:123413400-123449600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr12:123413600-123450000	Weak transcription	Primary T cells from cord blood	blood
5	chr12:123417400-123441800	Weak transcription	Ovary	ovary
6	chr12:123417600-123446200	Weak transcription	Fetal Lung	lung
7	chr12:123429600-123444000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:123429800-123444000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:123430000-123441800	Weak transcription	Fetal Brain Male	brain
10	chr12:123432000-123444000	Weak transcription	Thymus	Thymus
11	chr12:123432200-123441800	Weak transcription	Right Ventricle	heart
12	chr12:123432200-123444200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:123432200-123446000	Weak transcription	Right Atrium	heart
14	chr12:123432200-123446000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:123432200-123446000	Weak transcription	K562	blood
16	chr12:123432200-123450000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr12:123432200-123450200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:123432400-123444200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:123432400-123444200	Weak transcription	Pancreas	Pancrea
20	chr12:123432400-123448200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr12:123432400-123449600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr12:123432400-123450000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr12:123432600-123441600	Weak transcription	Lung	lung
24	chr12:123432600-123444200	Weak transcription	Esophagus	oesophagus
25	chr12:123432600-123444200	Weak transcription	Spleen	Spleen
26	chr12:123432600-123444400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:123432600-123448200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr12:123432600-123450000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr12:123433000-123441800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:123433200-123441800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:123434800-123441600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr12:123435000-123443000	Weak transcription	Brain Anterior Caudate	brain
33	chr12:123435200-123442800	Weak transcription	Brain Substantia Nigra	brain
34	chr12:123435200-123444200	Weak transcription	Gastric	stomach
35	chr12:123435400-123444000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr12:123436400-123441800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:123436400-123444000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr12:123436400-123444200	Weak transcription	NHLF	lung
39	chr12:123436400-123448000	Weak transcription	HepG2	liver
40	chr12:123436600-123441600	Weak transcription	Osteobl	bone
41	chr12:123436600-123444000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:123436600-123446000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr12:123436600-123446000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr12:123436600-123449400	Weak transcription	NHDF-Ad	bronchial
45	chr12:123436800-123441800	Weak transcription	HUVEC	blood vessel
46	chr12:123436800-123442800	Weak transcription	Fetal Intestine Large	intestine
47	chr12:123436800-123443800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:123436800-123444000	Weak transcription	HMEC	breast
49	chr12:123436800-123444400	Weak transcription	NHEK	skin
50	chr12:123436800-123446200	Weak transcription	A549	lung

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