Variant report

Variant	rs1480037
Chromosome Location	chr12:26277896-26277897
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	CTCF	chr12:26277820-26277970	GM12869	blood:	n/a	n/a
2	USF1	chr12:26277848-26278202	SK-N-SH_RA	brain:	n/a	chr12:26278009-26278022
3	BHLHE40	chr12:26277805-26278178	K562	blood:	n/a	chr12:26278009-26278022
4	EP300	chr12:26277880-26277907	GM12878	blood:	n/a	n/a
5	MYC	chr12:26277620-26279870	NB4	blood:	n/a	chr12:26279525-26279534 chr12:26277873-26277883 chr12:26278212-26278222 chr12:26279524-26279535 chr12:26278316-26278324 chr12:26279525-26279534
6	CTCF	chr12:26277800-26277950	HPAF	blood vessel:	n/a	n/a
7	MAX	chr12:26277686-26278170	A549	lung:	n/a	chr12:26277873-26277883
8	ZNF263	chr12:26277362-26278041	HEK293-T-REx	kidney:	n/a	chr12:26277819-26277840
9	MAX	chr12:26277719-26278074	GM12878	blood:	n/a	chr12:26277873-26277883
10	BHLHE40	chr12:26277742-26278210	HepG2	liver:	n/a	chr12:26278009-26278022
11	KAP1	chr12:26277403-26277953	HEK293	kidney:	n/a	n/a
12	ZNF143	chr12:26277842-26277937	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:26277218-26278349	SK-N-SH	brain:	n/a	n/a
14	CTCF	chr12:26277780-26277930	HUVEC	blood vessel:	n/a	n/a
15	MAX	chr12:26277378-26279826	NB4	blood:	n/a	chr12:26279525-26279534 chr12:26277873-26277883 chr12:26278212-26278222 chr12:26279524-26279535 chr12:26278316-26278324 chr12:26279525-26279534
16	USF1	chr12:26277843-26278196	SK-N-SH	brain:	n/a	chr12:26278009-26278022
17	CTCF	chr12:26277840-26277990	HEK293	kidney:	n/a	n/a
18	MYC	chr12:26277879-26278029	MCF-7	breast:	n/a	n/a
19	POLR2A	chr12:26277806-26279712	HEK293	kidney:	n/a	n/a
20	CTCF	chr12:26277843-26278042	GM19239	blood:	n/a	n/a
21	JUND	chr12:26277150-26280021	SK-N-SH	brain:	n/a	chr12:26277187-26277196 chr12:26278869-26278878 chr12:26279134-26279144 chr12:26279135-26279144 chr12:26278870-26278879 chr12:26278366-26278375 chr12:26279135-26279142 chr12:26277193-26277202 chr12:26277188-26277197 chr12:26277192-26277201 chr12:26279133-26279144 chr12:26279134-26279145
22	SIN3A	chr12:26277737-26279739	H1-hESC	embryonic stem cell:	n/a	chr12:26279511-26279522 chr12:26279605-26279619
23	CHD2	chr12:26277748-26278065	H1-hESC	embryonic stem cell:	n/a	n/a
24	CEBPB	chr12:26277878-26278078	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAZ	chr12:26277688-26278206	GM12878	blood:	n/a	chr12:26277873-26277883
26	POLR2A	chr12:26277856-26278041	HCT-116	colon:	n/a	n/a
27	CTCF	chr12:26277780-26277930	HCPEpiC	choroid plexus:	n/a	n/a
28	CTCF	chr12:26277820-26277970	SK-N-SH_RA	brain:	n/a	n/a
29	PBX3	chr12:26277700-26279795	SK-N-SH	brain:	n/a	n/a
30	CTCF	chr12:26277820-26277970	NHDF-neo	bronchial:	n/a	n/a
31	BHLHE40	chr12:26277643-26279750	GM12878	blood:	n/a	chr12:26279048-26279064 chr12:26278009-26278022 chr12:26279655-26279671 chr12:26279578-26279594 chr12:26279588-26279604 chr12:26279563-26279579 chr12:26279576-26279592
32	CTCF	chr12:26277880-26278030	BJ	skin:	n/a	n/a
33	GATA3	chr12:26277571-26279865	SK-N-SH	brain:	n/a	chr12:26278365-26278375
34	SIN3AK20	chr12:26277709-26278087	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr12:26277222-26278024	U87	brain:	n/a	n/a
36	BACH1	chr12:26277710-26278042	H1-hESC	embryonic stem cell:	n/a	n/a
37	MAX	chr12:26277717-26278248	HCT-116	colon:	n/a	chr12:26277873-26277883 chr12:26278212-26278222
38	MXI1	chr12:26277872-26278020	H1-hESC	embryonic stem cell:	n/a	n/a
39	SUZ12	chr12:26274316-26278522	NT2-D1	testis:	n/a	n/a
40	TCF7L2	chr12:26277741-26279758	HCT-116	colon:	n/a	n/a
41	CTCF	chr12:26277780-26277930	AoAF	blood vessel:	n/a	n/a
42	MAX	chr12:26277657-26278276	H1-hESC	embryonic stem cell:	n/a	chr12:26277873-26277883 chr12:26278212-26278222
43	E2F6	chr12:26277879-26278033	K562	blood:	n/a	n/a
44	MAX	chr12:26277891-26278039	K562	blood:	n/a	n/a
45	SIN3AK20	chr12:26277325-26279880	PANC-1	pancreas:	n/a	n/a
46	CTBP2	chr12:26277689-26279793	H1-hESC	embryonic stem cell:	n/a	n/a
47	MYC	chr12:26277801-26278122	MCF-7	breast:	n/a	chr12:26277873-26277883
48	POLR2A	chr12:26277202-26279995	U87	brain:	n/a	n/a
49	POLR2A	chr12:26277772-26278002	ProgFib	skin:	n/a	n/a
50	CTCF	chr12:26277800-26277950	BJ	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:26274388..26277209-chr12:26277264..26280315,5	K562	blood:

Variant related genes	Relation type
BHLHE41	TF binding region
ENSG00000123096	Chromatin interaction
ENSG00000123095	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11048402	1.00[ASW][hapmap];1.00[AFR][1000 genomes]
rs12318480	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12818979	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12822290	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12827659	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1531649	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17366300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17366955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17367221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17380333	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17380416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17463675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17464133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17464383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1871557	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4963650	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4963958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4963960	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4963962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4963965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4963966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4963970	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57749967	0.87[ASN][1000 genomes]
rs57948457	0.87[ASN][1000 genomes]
rs58269831	1.00[ASN][1000 genomes]
rs58769131	0.87[ASN][1000 genomes]
rs61139398	0.87[ASN][1000 genomes]
rs7358598	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898932	chr12:26262137-26283482	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv898933	chr12:26262137-26285006	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26272200-26280000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:26273000-26280000	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr12:26273400-26280000	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr12:26273400-26280000	Active TSS	Right Atrium	heart
5	chr12:26273600-26279800	Active TSS	Psoas Muscle	Psoas
6	chr12:26273600-26280000	Active TSS	Brain Substantia Nigra	brain
7	chr12:26274000-26280000	Active TSS	Brain Angular Gyrus	brain
8	chr12:26274200-26279600	Active TSS	Colon Smooth Muscle	Colon
9	chr12:26274400-26279800	Active TSS	NHDF-Ad	bronchial
10	chr12:26274400-26280200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr12:26274600-26280000	Active TSS	Aorta	Aorta
12	chr12:26274600-26280000	Active TSS	Right Ventricle	heart
13	chr12:26274600-26280000	Active TSS	HSMM	muscle
14	chr12:26274800-26279800	Active TSS	Left Ventricle	heart
15	chr12:26274800-26280000	Active TSS	Ovary	ovary
16	chr12:26275000-26279800	Active TSS	Brain Anterior Caudate	brain
17	chr12:26275000-26279800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
18	chr12:26275000-26280000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:26275000-26280000	Active TSS	Brain Cingulate Gyrus	brain
20	chr12:26275000-26280400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:26275600-26278800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:26276000-26278000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
23	chr12:26276000-26278000	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
24	chr12:26276200-26278200	Bivalent/Poised TSS	Thymus	Thymus
25	chr12:26276600-26279800	Active TSS	Brain Hippocampus Middle	brain
26	chr12:26276600-26279800	Active TSS	Rectal Smooth Muscle	rectum
27	chr12:26276800-26279600	Active TSS	HMEC	breast
28	chr12:26276800-26279800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:26276800-26279800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:26276800-26279800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
31	chr12:26276800-26280000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
32	chr12:26277000-26279800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:26277000-26279800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
34	chr12:26277200-26278000	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
35	chr12:26277200-26278000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:26277200-26278400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
37	chr12:26277200-26278400	Active TSS	Stomach Smooth Muscle	stomach
38	chr12:26277200-26279000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
39	chr12:26277200-26279400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
40	chr12:26277400-26278000	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:26277400-26278000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:26277400-26278000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:26277400-26278000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:26277400-26278000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
45	chr12:26277400-26278000	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
46	chr12:26277400-26278000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
47	chr12:26277400-26278000	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
48	chr12:26277400-26278000	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:26277400-26278000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:26277400-26278000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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