Variant report

Variant	rs1383116
Chromosome Location	chr12:26278079-26278080
allele	G/T
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	chr12:26277960-26278110	GM12868	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	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
5	MAX	chr12:26277686-26278170	A549	lung:	n/a	chr12:26277873-26277883
6	BHLHE40	chr12:26277742-26278210	HepG2	liver:	n/a	chr12:26278009-26278022
7	POLR2A	chr12:26277218-26278349	SK-N-SH	brain:	n/a	n/a
8	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
9	USF1	chr12:26277843-26278196	SK-N-SH	brain:	n/a	chr12:26278009-26278022
10	POLR2A	chr12:26277806-26279712	HEK293	kidney:	n/a	n/a
11	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
12	JUND	chr12:26277946-26278129	H1-hESC	embryonic stem cell:	n/a	n/a
13	SIN3A	chr12:26277737-26279739	H1-hESC	embryonic stem cell:	n/a	chr12:26279511-26279522 chr12:26279605-26279619
14	MAZ	chr12:26277688-26278206	GM12878	blood:	n/a	chr12:26277873-26277883
15	PBX3	chr12:26277700-26279795	SK-N-SH	brain:	n/a	n/a
16	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
17	GATA3	chr12:26277571-26279865	SK-N-SH	brain:	n/a	chr12:26278365-26278375
18	RAD21	chr12:26278073-26278330	SK-N-SH_RA	brain:	n/a	n/a
19	SIN3AK20	chr12:26277709-26278087	SK-N-SH	brain:	n/a	n/a
20	MAX	chr12:26277717-26278248	HCT-116	colon:	n/a	chr12:26277873-26277883 chr12:26278212-26278222
21	SUZ12	chr12:26274316-26278522	NT2-D1	testis:	n/a	n/a
22	TCF7L2	chr12:26277741-26279758	HCT-116	colon:	n/a	n/a
23	MAX	chr12:26277657-26278276	H1-hESC	embryonic stem cell:	n/a	chr12:26277873-26277883 chr12:26278212-26278222
24	SIN3AK20	chr12:26277325-26279880	PANC-1	pancreas:	n/a	n/a
25	CTBP2	chr12:26277689-26279793	H1-hESC	embryonic stem cell:	n/a	n/a
26	MYC	chr12:26277801-26278122	MCF-7	breast:	n/a	chr12:26277873-26277883
27	POLR2A	chr12:26277202-26279995	U87	brain:	n/a	n/a
28	E2F6	chr12:26277615-26278239	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr12:26277232-26279832	H1-neurons	neurons:	n/a	n/a
30	CTCF	chr12:26278020-26278170	HUVEC	blood vessel:	n/a	n/a
31	MAX	chr12:26277629-26279915	ECC-1	luminal epithelium:	n/a	chr12:26279525-26279534 chr12:26277873-26277883 chr12:26278212-26278222 chr12:26279524-26279535 chr12:26278316-26278324 chr12:26279525-26279534
32	JUND	chr12:26277868-26278195	H1-hESC	embryonic stem cell:	n/a	n/a
33	EP300	chr12:26277825-26278277	SK-N-SH_RA	brain:	n/a	chr12:26277924-26277940
34	MAX	chr12:26277683-26279888	ECC-1	luminal epithelium:	n/a	chr12:26279525-26279534 chr12:26277873-26277883 chr12:26278212-26278222 chr12:26279524-26279535 chr12:26278316-26278324 chr12:26279525-26279534
35	POLR2A	chr12:26277202-26280295	H1-neurons	neurons:	n/a	n/a
36	POLR2A	chr12:26275569-26280099	PANC-1	pancreas:	n/a	n/a
37	MAX	chr12:26277504-26278372	SK-N-SH	brain:	n/a	chr12:26277873-26277883 chr12:26278212-26278222 chr12:26278316-26278324
38	MAX	chr12:26277808-26278629	H1-hESC	embryonic stem cell:	n/a	chr12:26277873-26277883 chr12:26278212-26278222 chr12:26278316-26278324
39	MAX	chr12:26277611-26279847	SK-N-SH	brain:	n/a	chr12:26279525-26279534 chr12:26277873-26277883 chr12:26278212-26278222 chr12:26279524-26279535 chr12:26278316-26278324 chr12:26279525-26279534
40	POLR2A	chr12:26278076-26279859	U87	brain:	n/a	n/a
41	TCF7L2	chr12:26277342-26280013	PANC-1	pancreas:	n/a	n/a
42	REST	chr12:26277755-26278162	PANC-1	pancreas:	n/a	n/a
43	MAX	chr12:26277548-26279926	A549	lung:	n/a	chr12:26279525-26279534 chr12:26277873-26277883 chr12:26278212-26278222 chr12:26279524-26279535 chr12:26278316-26278324 chr12:26279525-26279534
44	USF1	chr12:26277851-26278150	SK-N-SH_RA	brain:	n/a	chr12:26278009-26278022
45	POLR2A	chr12:26274089-26279927	PANC-1	pancreas:	n/a	n/a
46	USF1	chr12:26277812-26278205	ECC-1	luminal epithelium:	n/a	chr12:26278009-26278022
47	FOXP2	chr12:26277787-26278099	PFSK-1	brain:	n/a	n/a
48	E2F6	chr12:26277687-26278236	H1-hESC	embryonic stem cell:	n/a	n/a
49	CHD2	chr12:26277817-26278191	GM12878	blood:	n/a	n/a
50	MAX	chr12:26277519-26278518	H1-hESC	embryonic stem cell:	n/a	chr12:26277873-26277883 chr12:26278212-26278222 chr12:26278316-26278324

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
ENSG00000123095	Chromatin interaction
ENSG00000123096	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10771262	0.80[AFR][1000 genomes]
rs10842679	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10842680	0.83[AFR][1000 genomes]
rs1383112	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1383113	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2729628	0.80[AMR][1000 genomes]
rs3809140	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6487532	0.83[AFR][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	chr12:26276200-26278200	Bivalent/Poised TSS	Thymus	Thymus
23	chr12:26276600-26279800	Active TSS	Brain Hippocampus Middle	brain
24	chr12:26276600-26279800	Active TSS	Rectal Smooth Muscle	rectum
25	chr12:26276800-26279600	Active TSS	HMEC	breast
26	chr12:26276800-26279800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:26276800-26279800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:26276800-26279800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
29	chr12:26276800-26280000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
30	chr12:26277000-26279800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:26277000-26279800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
32	chr12:26277200-26278400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
33	chr12:26277200-26278400	Active TSS	Stomach Smooth Muscle	stomach
34	chr12:26277200-26279000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
35	chr12:26277200-26279400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
36	chr12:26277400-26278400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
37	chr12:26277400-26278800	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr12:26277400-26279600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
39	chr12:26277400-26279800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:26277400-26279800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
41	chr12:26277600-26278600	Bivalent Enhancer	K562	blood
42	chr12:26277600-26279600	Active TSS	Esophagus	oesophagus
43	chr12:26277600-26279600	Active TSS	Placenta Amnion	Placenta Amnion
44	chr12:26277600-26279800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr12:26277800-26278200	Bivalent Enhancer	Fetal Brain Male	brain
46	chr12:26277800-26278200	Bivalent Enhancer	Fetal Heart	heart
47	chr12:26277800-26278200	Enhancers	Hela-S3	cervix
48	chr12:26277800-26278400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
49	chr12:26277800-26278400	Bivalent/Poised TSS	Fetal Brain Female	brain
50	chr12:26277800-26278400	Active TSS	Skeletal Muscle Female	skeletal muscle

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