Variant report

Variant	rs3764024
Chromosome Location	chr12:9801373-9801374
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	MXI1	chr12:9800287-9802771	GM12878	blood:	n/a	n/a
2	TCF7L2	chr12:9801004-9801504	MCF-7	breast:	n/a	n/a
3	UBTF	chr12:9800050-9801395	K562	blood:	n/a	n/a
4	STAT3	chr12:9800692-9801447	GM12878	blood:	n/a	chr12:9800768-9800780
5	BRCA1	chr12:9800286-9801460	Hela-S3	cervix:	n/a	n/a
6	CHD1	chr12:9800337-9804156	GM12878	blood:	n/a	chr12:9800667-9800677 chr12:9800660-9800670
7	TBL1XR1	chr12:9799984-9802966	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:9799451-9804403	GM19193	blood:	n/a	n/a
9	TBP	chr12:9800698-9801701	GM12878	blood:	n/a	n/a
10	EP300	chr12:9800236-9801592	ECC-1	luminal epithelium:	n/a	chr12:9800672-9800688 chr12:9800673-9800689
11	RUNX3	chr12:9799672-9801651	GM12878	blood:	n/a	chr12:9800805-9800822
12	MTA3	chr12:9799406-9804477	GM12878	blood:	n/a	n/a
13	MAX	chr12:9800358-9801415	SK-N-SH	brain:	n/a	n/a
14	EP300	chr12:9800363-9802584	GM12878	blood:	n/a	chr12:9801950-9801964 chr12:9802375-9802389 chr12:9800672-9800688 chr12:9800673-9800689
15	EP300	chr12:9800947-9801544	MCF-7	breast:	n/a	n/a
16	EP300	chr12:9800520-9802522	GM12878	blood:	n/a	chr12:9801950-9801964 chr12:9802375-9802389 chr12:9800672-9800688 chr12:9800673-9800689
17	POLR2A	chr12:9800075-9801532	U87	brain:	n/a	n/a
18	RUNX3	chr12:9799645-9802568	GM12878	blood:	n/a	chr12:9800805-9800822
19	BHLHE40	chr12:9800302-9801534	K562	blood:	n/a	chr12:9800672-9800688 chr12:9800678-9800694
20	POLR2A	chr12:9799501-9804451	GM12891	blood:	n/a	n/a
21	IRF1	chr12:9799891-9802485	K562	blood:	n/a	chr12:9801699-9801712 chr12:9802381-9802392 chr12:9801697-9801711 chr12:9802380-9802394 chr12:9800630-9800644 chr12:9801698-9801711 chr12:9801737-9801744 chr12:9801701-9801712 chr12:9801702-9801712 chr12:9801699-9801713 chr12:9801700-9801714 chr12:9801698-9801712 chr12:9801699-9801713
22	KAP1	chr12:9799906-9802085	U2OS	brain:	n/a	chr12:9800521-9800529
23	POLR2A	chr12:9799408-9804409	GM19099	blood:	n/a	n/a
24	POLR2A	chr12:9799796-9802695	HepG2	liver:	n/a	n/a
25	MAZ	chr12:9799597-9801421	K562	blood:	n/a	n/a
26	NR2F2	chr12:9800908-9801550	MCF-7	breast:	n/a	n/a
27	EP300	chr12:9800439-9801783	GM12878	blood:	n/a	chr12:9800672-9800688 chr12:9800673-9800689
28	SIN3AK20	chr12:9800262-9801561	MCF-7	breast:	n/a	n/a
29	HEY1	chr12:9800213-9801473	HepG2	liver:	n/a	n/a
30	POLR2A	chr12:9800290-9801652	GM12891	blood:	n/a	n/a
31	GATA3	chr12:9801056-9801477	MCF-7	breast:	n/a	n/a
32	POLR2A	chr12:9799794-9802049	IMR90	lung:	n/a	n/a
33	KAP1	chr12:9799923-9802306	HEK293	kidney:	n/a	chr12:9800521-9800529
34	POLR2A	chr12:9799328-9804610	GM12878	blood:	n/a	n/a
35	CHD2	chr12:9800272-9801398	K562	blood:	n/a	chr12:9800667-9800677 chr12:9800660-9800670
36	TAF1	chr12:9800220-9801403	ECC-1	luminal epithelium:	n/a	n/a
37	ATF2	chr12:9800087-9804473	GM12878	blood:	n/a	n/a
38	POLR2A	chr12:9800142-9804355	GM18951	blood:	n/a	n/a
39	EGR1	chr12:9800970-9801467	MCF-7	breast:	n/a	n/a
40	POLR2A	chr12:9800745-9801580	GM12891	blood:	n/a	n/a
41	POLR2A	chr12:9799314-9804469	GM12892	blood:	n/a	n/a
42	FOXM1	chr12:9800251-9801779	GM12878	blood:	n/a	n/a
43	EP300	chr12:9800351-9801455	K562	blood:	n/a	chr12:9800672-9800688 chr12:9800673-9800689
44	TBP	chr12:9800413-9801416	K562	blood:	n/a	n/a
45	POLR2A	chr12:9799782-9803691	NB4	blood:	n/a	n/a
46	GTF2F1	chr12:9801331-9801417	H1-hESC	embryonic stem cell:	n/a	n/a
47	BCLAF1	chr12:9800289-9801692	GM12878	blood:	n/a	chr12:9800683-9800696 chr12:9800565-9800578
48	POLR2A	chr12:9800275-9801442	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr12:9800211-9801401	ECC-1	luminal epithelium:	n/a	n/a
50	CHD2	chr12:9800468-9801414	Hela-S3	cervix:	n/a	chr12:9800667-9800677 chr12:9800660-9800670

No.	Distal block	Cell Line	Cell type
1	chr12:9801129..9802680-chr12:9843178..9846016,2	K562	blood:
2	chr12:9801303..9803979-chr12:9875830..9877610,2	K562	blood:
3	chr12:9799292..9802850-chr12:9823422..9827161,3	MCF-7	breast:
4	chr12:9801031..9803712-chr12:9946954..9949811,3	K562	blood:
5	chr12:9739995..9741756-chr12:9800822..9803051,2	K562	blood:
6	chr12:9800923..9803675-chr12:9838767..9841892,3	MCF-7	breast:
7	chr12:9800782..9802831-chr12:9859086..9861954,2	MCF-7	breast:
8	chr12:9799323..9802837-chr12:9803671..9808302,9	K562	blood:
9	chr12:9600285..9602561-chr12:9801026..9803503,2	K562	blood:
10	chr12:9800783..9805047-chr12:9809567..9813940,5	K562	blood:
11	chr12:9786143..9793024-chr12:9797652..9803573,13	MCF-7	breast:
12	chr12:9799537..9802341-chr12:9814175..9817797,3	K562	blood:
13	chr12:9798786..9803516-chr12:9803864..9807970,10	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLEC2D-8	chr12:9800643-9801529	NONHSAT026839
2	lnc-CLEC2D-8	chr12:9800643-9801529	NONHSAT026843

Variant related genes	Relation type
ENSG00000256594	TF binding region
ENSG00000256442	TF binding region
ENSG00000069493	Chromatin interaction
ENSG00000256594	Chromatin interaction
ENSG00000214826	Chromatin interaction
ENSG00000257027	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10047657	0.97[ASN][1000 genomes]
rs10743806	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10771987	0.91[ASN][1000 genomes]
rs10772001	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10772010	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10844325	0.97[ASN][1000 genomes]
rs10844373	0.97[ASN][1000 genomes]
rs1560007	0.93[ASN][1000 genomes]
rs17805558	0.89[ASN][1000 genomes]
rs1863873	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1863874	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34383380	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3764023	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131784	0.91[ASN][1000 genomes]
rs7299076	0.93[ASN][1000 genomes]
rs7313927	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7316121	0.91[ASN][1000 genomes]
rs7959272	0.89[ASN][1000 genomes]
rs7975716	0.89[ASN][1000 genomes]
rs969367	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv2757489	chr12:9583455-9810764	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv917178	chr12:9637315-9820153	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 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	chr12:9799800-9801400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:9799800-9801800	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr12:9799800-9802200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr12:9799800-9803600	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr12:9800000-9801800	Active TSS	H1 Cell Line	embryonic stem cell
6	chr12:9800000-9801800	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr12:9800000-9802000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:9800000-9802000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:9800000-9802000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:9800000-9802200	Active TSS	Brain Germinal Matrix	brain
11	chr12:9800000-9802800	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr12:9800000-9802800	Active TSS	Fetal Kidney	kidney
13	chr12:9800000-9803400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:9800000-9803600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:9800000-9804000	Active TSS	Rectal Smooth Muscle	rectum
16	chr12:9800200-9801400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:9800200-9801400	Flanking Active TSS	Liver	Liver
18	chr12:9800200-9801600	Active TSS	Gastric	stomach
19	chr12:9800200-9801800	Active TSS	H9 Cell Line	embryonic stem cell
20	chr12:9800200-9801800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:9800200-9801800	Active TSS	A549	lung
22	chr12:9800200-9802000	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr12:9800200-9802000	Active TSS	Fetal Intestine Small	intestine
24	chr12:9800200-9802000	Active TSS	Left Ventricle	heart
25	chr12:9800200-9802000	Active TSS	Psoas Muscle	Psoas
26	chr12:9800200-9802200	Active TSS	Aorta	Aorta
27	chr12:9800200-9802200	Active TSS	Brain Cingulate Gyrus	brain
28	chr12:9800200-9802200	Flanking Active TSS	HMEC	breast
29	chr12:9800200-9802400	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr12:9800200-9802400	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr12:9800200-9802400	Flanking Active TSS	HUVEC	blood vessel
32	chr12:9800200-9802600	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr12:9800200-9802600	Active TSS	Colon Smooth Muscle	Colon
34	chr12:9800200-9802600	Active TSS	Ovary	ovary
35	chr12:9800200-9802800	Active TSS	NHDF-Ad	bronchial
36	chr12:9800200-9803400	Active TSS	Brain Anterior Caudate	brain
37	chr12:9800200-9803400	Active TSS	Esophagus	oesophagus
38	chr12:9800200-9803400	Active TSS	Right Ventricle	heart
39	chr12:9800200-9803400	Active TSS	HSMMtube	muscle
40	chr12:9800200-9803600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:9800200-9804000	Active TSS	Right Atrium	heart
42	chr12:9800400-9801400	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr12:9800400-9801600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:9800400-9801600	Active TSS	Fetal Brain Male	brain
45	chr12:9800400-9801600	Bivalent/Poised TSS	HepG2	liver
46	chr12:9800400-9801800	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr12:9800400-9801800	Active TSS	Fetal Stomach	stomach
48	chr12:9800400-9802000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr12:9800400-9802000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr12:9800400-9802000	Active TSS	Fetal Intestine Large	intestine

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