Variant report

Variant	rs4072006
Chromosome Location	chr12:40014427-40014428
allele	A/G
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	RELA	chr12:40011625-40014816	GM18505	blood:	n/a	n/a
2	MTA3	chr12:40012433-40014859	GM12878	blood:	n/a	n/a
3	EBF1	chr12:40013089-40014798	GM12878	blood:	n/a	n/a
4	EP300	chr12:40013301-40014631	GM12878	blood:	n/a	chr12:40014211-40014225
5	POLR2A	chr12:40011748-40015954	GM12878	blood:	n/a	n/a
6	MAZ	chr12:40013491-40014851	GM12878	blood:	n/a	n/a
7	BHLHE40	chr12:40013084-40014481	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:40011711-40015724	GM19193	blood:	n/a	n/a
9	POLR2A	chr12:40011618-40015633	GM12891	blood:	n/a	n/a
10	POLR2A	chr12:40011640-40015813	GM18505	blood:	n/a	n/a
11	RCOR1	chr12:40013230-40014876	K562	blood:	n/a	n/a
12	TBL1XR1	chr12:40012952-40014737	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:40011695-40015642	GM12892	blood:	n/a	n/a
14	STAT3	chr12:40013090-40014783	GM12878	blood:	n/a	chr12:40014657-40014664 chr12:40014769-40014776 chr12:40014210-40014221
15	RFX5	chr12:40013606-40014647	Hela-S3	cervix:	n/a	chr12:40013663-40013672
16	MTA3	chr12:40012267-40015651	GM12878	blood:	n/a	n/a
17	RUNX3	chr12:40012904-40014871	GM12878	blood:	n/a	n/a
18	ZNF263	chr12:40013184-40014742	HEK293-T-REx	kidney:	n/a	chr12:40013644-40013653 chr12:40014140-40014149 chr12:40014103-40014124
19	POLR2A	chr12:40012795-40014785	GM12892	blood:	n/a	n/a
20	POLR2A	chr12:40011695-40015585	GM19099	blood:	n/a	n/a
21	PML	chr12:40012932-40015655	GM12878	blood:	n/a	n/a
22	ATF2	chr12:40013016-40014468	GM12878	blood:	n/a	n/a
23	NFIC	chr12:40011603-40015858	GM12878	blood:	n/a	n/a
24	KAP1	chr12:40013160-40014813	HEK293	kidney:	n/a	n/a
25	POLR2A	chr12:40011409-40015472	GM12878	blood:	n/a	n/a
26	MXI1	chr12:40011430-40015371	SK-N-SH	brain:	n/a	n/a
27	CEBPB	chr12:40013272-40015600	GM12878	blood:	n/a	chr12:40013664-40013672
28	POLR2A	chr12:40012304-40014704	GM12878	blood:	n/a	n/a
29	CHD1	chr12:40012703-40014800	GM12878	blood:	n/a	n/a
30	IKZF1	chr12:40012632-40014760	GM12878	blood:	n/a	n/a
31	STAT5A	chr12:40012947-40014601	GM12878	blood:	n/a	chr12:40014210-40014221
32	POLR2A	chr12:40012209-40015633	GM12892	blood:	n/a	n/a
33	TBP	chr12:40012430-40016676	GM12878	blood:	n/a	n/a
34	POLR2A	chr12:40012286-40014812	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40014171..40017168-chr12:40017549..40021409,3	K562	blood:
2	chr12:40010562..40012556-chr12:40014262..40016328,2	K562	blood:

Variant related genes	Relation type
ABCD2	TF binding region
ENSG00000180116	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10877173	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10877201	0.81[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs11172144	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11172162	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11172366	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172480	0.80[ASN][1000 genomes]
rs11172616	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172645	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172646	0.86[ASN][1000 genomes]
rs11172647	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172687	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11172692	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172697	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172713	0.83[CEU][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs11172722	0.88[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172794	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172848	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11172896	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172897	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12227286	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12227668	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12228013	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12228617	0.86[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs12229160	0.83[EUR][1000 genomes]
rs12229370	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12230055	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12231004	0.83[ASN][1000 genomes]
rs17127129	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs17127138	0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs35790935	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35858791	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4285917	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4294600	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4298947	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4639970	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57847223	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58036566	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59518553	0.86[ASN][1000 genomes]
rs59528535	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61258856	0.81[EUR][1000 genomes]
rs6581228	0.86[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs7133376	0.83[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap]
rs7133599	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7134015	0.83[ASN][1000 genomes]
rs7294474	0.81[EUR][1000 genomes]
rs7302302	0.81[EUR][1000 genomes]
rs7307784	0.83[ASN][1000 genomes]
rs73088816	0.81[EUR][1000 genomes]
rs7309234	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73094447	0.81[EUR][1000 genomes]
rs73094449	0.81[EUR][1000 genomes]
rs73094488	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7310178	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7310871	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7312611	0.88[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap]
rs73268358	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73268359	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74086536	0.81[EUR][1000 genomes]
rs7970944	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1037457	chr12:39898349-40245401	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers 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	9 gene(s)	inside rSNPs	diseases
3	nsv541480	chr12:39898349-40245401	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1039645	chr12:39903123-40022029	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv469359	chr12:39946354-40034699	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv558591	chr12:39946354-40034699	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv469361	chr12:39946354-40042220	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv558592	chr12:39946354-40042220	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv899014	chr12:39946354-40068896	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv899015	chr12:39946354-40118249	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv899017	chr12:39949147-40081619	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
12	nsv899018	chr12:39949147-40111761	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
13	nsv899020	chr12:39985206-40040331	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv899021	chr12:39989172-40053423	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv899022	chr12:40014427-40111761	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4072006	ABCD2	cis	multi-tissue	Pritchard

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40006800-40015000	Active TSS	GM12878-XiMat	blood
2	chr12:40009400-40015400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr12:40009600-40014800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:40009600-40015000	Active TSS	Primary T killer memory cells from peripheral blood	blood
5	chr12:40009800-40014800	Active TSS	Brain Angular Gyrus	brain
6	chr12:40009800-40015000	Active TSS	Primary T cells fromperipheralblood	blood
7	chr12:40009800-40015000	Active TSS	Primary T helper naive cells from peripheral blood	blood
8	chr12:40009800-40015200	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr12:40009800-40015200	Active TSS	Right Atrium	heart
10	chr12:40010200-40014600	Active TSS	Brain Germinal Matrix	brain
11	chr12:40010800-40015000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:40011800-40015200	Active TSS	Brain Cingulate Gyrus	brain
13	chr12:40012000-40014600	Active TSS	Brain Substantia Nigra	brain
14	chr12:40012200-40014600	Active TSS	Colon Smooth Muscle	Colon
15	chr12:40012400-40014600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:40012600-40014600	Active TSS	Right Ventricle	heart
17	chr12:40012600-40014800	Active TSS	Psoas Muscle	Psoas
18	chr12:40012600-40015000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:40012600-40015200	Active TSS	Colonic Mucosa	Colon
20	chr12:40012800-40014600	Active TSS	Fetal Brain Female	brain
21	chr12:40012800-40014600	Active TSS	Thymus	Thymus
22	chr12:40012800-40014800	Active TSS	Muscle Satellite Cultured Cells	--
23	chr12:40012800-40014800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:40012800-40014800	Active TSS	Brain Hippocampus Middle	brain
25	chr12:40012800-40014800	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr12:40012800-40015000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:40012800-40015200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr12:40013000-40014600	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr12:40013000-40014600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:40013000-40014600	Active TSS	Ovary	ovary
31	chr12:40013000-40014800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:40013000-40014800	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr12:40013000-40014800	Active TSS	Fetal Brain Male	brain
34	chr12:40013000-40014800	Active TSS	HSMMtube	muscle
35	chr12:40013000-40015000	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr12:40013000-40015200	Active TSS	Rectal Smooth Muscle	rectum
37	chr12:40013200-40014600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr12:40013200-40014600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr12:40013200-40014600	Active TSS	Brain Anterior Caudate	brain
40	chr12:40013200-40014600	Active TSS	Fetal Thymus	thymus
41	chr12:40013200-40014800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:40013200-40014800	Active TSS	Aorta	Aorta
43	chr12:40013200-40014800	Active TSS	Stomach Smooth Muscle	stomach
44	chr12:40013200-40015000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:40013200-40015200	Active TSS	Duodenum Mucosa	Duodenum
46	chr12:40013400-40014600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:40013400-40014600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:40013400-40014600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:40013400-40014600	Flanking Active TSS	Liver	Liver
50	chr12:40013400-40014600	Active TSS	Fetal Intestine Small	intestine

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