Variant report

Variant	rs3809140
Chromosome Location	chr12:26278444-26278445
allele	C/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	HA-E2F1	chr12:26278327-26279859	MCF-7	breast:	n/a	chr12:26279497-26279509 chr12:26279508-26279518 chr12:26279659-26279669 chr12:26278868-26278877 chr12:26279656-26279666 chr12:26279058-26279068
2	CEBPB	chr12:26278319-26278768	MCF-7	breast:	n/a	chr12:26278558-26278569
3	CEBPB	chr12:26278343-26278707	ECC-1	luminal epithelium:	n/a	chr12:26278558-26278569
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	SMC3	chr12:26278373-26279819	Hela-S3	cervix:	n/a	n/a
6	E2F6	chr12:26278326-26279896	A549	lung:	n/a	chr12:26279497-26279509 chr12:26279508-26279518 chr12:26279659-26279669 chr12:26278868-26278877 chr12:26279656-26279666 chr12:26279058-26279068
7	WRNIP1	chr12:26278380-26278572	GM12878	blood:	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	CEBPB	chr12:26278392-26278728	K562	blood:	n/a	chr12:26278558-26278569
10	CEBPB	chr12:26278359-26278807	A549	lung:	n/a	chr12:26278558-26278569
11	GTF2F1	chr12:26278354-26278637	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr12:26277806-26279712	HEK293	kidney:	n/a	n/a
13	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
14	ZNF263	chr12:26278292-26279795	HEK293-T-REx	kidney:	n/a	chr12:26279548-26279557 chr12:26279516-26279525
15	SIN3A	chr12:26277737-26279739	H1-hESC	embryonic stem cell:	n/a	chr12:26279511-26279522 chr12:26279605-26279619
16	REST	chr12:26278264-26278786	PANC-1	pancreas:	n/a	n/a
17	CEBPB	chr12:26278377-26278754	IMR90	lung:	n/a	chr12:26278558-26278569
18	SIN3AK20	chr12:26278322-26279591	PANC-1	pancreas:	n/a	n/a
19	PBX3	chr12:26277700-26279795	SK-N-SH	brain:	n/a	n/a
20	TCF12	chr12:26278328-26279802	ECC-1	luminal epithelium:	n/a	chr12:26279420-26279430 chr12:26278428-26278437
21	MXI1	chr12:26278250-26279939	SK-N-SH	brain:	n/a	n/a
22	RCOR1	chr12:26278420-26279766	Hela-S3	cervix:	n/a	n/a
23	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
24	CEBPB	chr12:26278365-26278747	A549	lung:	n/a	chr12:26278558-26278569
25	GATA3	chr12:26277571-26279865	SK-N-SH	brain:	n/a	chr12:26278365-26278375
26	ZKSCAN1	chr12:26278427-26278745	Hela-S3	cervix:	n/a	n/a
27	MAX	chr12:26278325-26280026	HCT-116	colon:	n/a	chr12:26279525-26279534 chr12:26279524-26279535 chr12:26279525-26279534
28	TEAD4	chr12:26278135-26279320	ECC-1	luminal epithelium:	n/a	chr12:26278305-26278314
29	SUZ12	chr12:26274316-26278522	NT2-D1	testis:	n/a	n/a
30	TCF7L2	chr12:26277741-26279758	HCT-116	colon:	n/a	n/a
31	CEBPB	chr12:26278394-26278751	HepG2	liver:	n/a	chr12:26278558-26278569
32	SIN3AK20	chr12:26277325-26279880	PANC-1	pancreas:	n/a	n/a
33	RFX5	chr12:26278379-26279673	Hela-S3	cervix:	n/a	n/a
34	CEBPB	chr12:26278354-26278731	H1-hESC	embryonic stem cell:	n/a	chr12:26278558-26278569
35	CTBP2	chr12:26277689-26279793	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr12:26278273-26278512	SK-N-SH	brain:	n/a	n/a
37	CEBPB	chr12:26278264-26278810	ECC-1	luminal epithelium:	n/a	chr12:26278558-26278569
38	POLR2A	chr12:26277202-26279995	U87	brain:	n/a	n/a
39	SMARCB1	chr12:26278375-26279774	Hela-S3	cervix:	n/a	n/a
40	SPI1	chr12:26278268-26278488	GM12891	blood:	n/a	chr12:26278368-26278377
41	MAX	chr12:26278366-26279839	A549	lung:	n/a	chr12:26279525-26279534 chr12:26279524-26279535 chr12:26279525-26279534
42	POLR2A	chr12:26277232-26279832	H1-neurons	neurons:	n/a	n/a
43	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
44	CEBPB	chr12:26278363-26279658	Hela-S3	cervix:	n/a	chr12:26278558-26278569
45	CHD2	chr12:26278181-26279763	Hela-S3	cervix:	n/a	n/a
46	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
47	POLR2A	chr12:26277202-26280295	H1-neurons	neurons:	n/a	n/a
48	TCF12	chr12:26278241-26278942	A549	lung:	n/a	chr12:26278428-26278437
49	POLR2A	chr12:26278389-26279729	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr12:26275569-26280099	PANC-1	pancreas:	n/a	n/a

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BHLHE41-1	chr12:26278439-26278514	ENSG00000256894.1
2	lnc-BHLHE41-1	chr12:26278439-26278685	ENSG00000256894.1

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

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10431216	0.82[CEU][hapmap]
rs10771262	0.82[AFR][1000 genomes]
rs10842679	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10842680	0.85[AFR][1000 genomes]
rs1383112	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.85[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1383113	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1383116	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2729628	0.83[AMR][1000 genomes]
rs6487532	0.85[AFR][1000 genomes];0.81[AMR][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:127 , 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	chr12:26276600-26279800	Active TSS	Brain Hippocampus Middle	brain
23	chr12:26276600-26279800	Active TSS	Rectal Smooth Muscle	rectum
24	chr12:26276800-26279600	Active TSS	HMEC	breast
25	chr12:26276800-26279800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:26276800-26279800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:26276800-26279800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
28	chr12:26276800-26280000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
29	chr12:26277000-26279800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:26277000-26279800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
31	chr12:26277200-26279000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
32	chr12:26277200-26279400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
33	chr12:26277400-26278800	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr12:26277400-26279600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
35	chr12:26277400-26279800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr12:26277400-26279800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
37	chr12:26277600-26278600	Bivalent Enhancer	K562	blood
38	chr12:26277600-26279600	Active TSS	Esophagus	oesophagus
39	chr12:26277600-26279600	Active TSS	Placenta Amnion	Placenta Amnion
40	chr12:26277600-26279800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr12:26277800-26278600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
42	chr12:26277800-26278600	Bivalent/Poised TSS	Fetal Kidney	kidney
43	chr12:26277800-26278800	Bivalent/Poised TSS	A549	lung
44	chr12:26277800-26279000	Active TSS	Duodenum Mucosa	Duodenum
45	chr12:26277800-26279200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:26277800-26279200	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr12:26277800-26279600	Active TSS	Muscle Satellite Cultured Cells	--
48	chr12:26277800-26279600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:26277800-26279600	Enhancers	Spleen	Spleen
50	chr12:26277800-26279800	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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