Variant report

Variant	rs58831065
Chromosome Location	chr6:12014144-12014145
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	CEBPB	chr6:12012920-12014899	Hela-S3	cervix:	n/a	chr6:12013068-12013079 chr6:12013652-12013669
2	POLR2A	chr6:12012916-12015805	HepG2	liver:	n/a	n/a
3	GATA3	chr6:12014062-12014984	MCF-7	breast:	n/a	chr6:12014952-12014959 chr6:12014952-12014959 chr6:12014515-12014524 chr6:12014952-12014959
4	POLR2A	chr6:12007817-12015834	GM12878	blood:	n/a	n/a
5	GTF3C2	chr6:12013587-12014703	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr6:12008239-12015396	IMR90	lung:	n/a	n/a
7	GATA3	chr6:12014034-12014517	SH-SY5Y	brain:	n/a	n/a
8	GATA3	chr6:12014031-12014908	A549	lung:	n/a	chr6:12014515-12014524
9	POLR2A	chr6:12012145-12015603	GM12892	blood:	n/a	n/a
10	POLR2A	chr6:12010517-12015551	HepG2	liver:	n/a	n/a
11	POLR2A	chr6:12008323-12014175	GM18505	blood:	n/a	n/a
12	GATA3	chr6:12014059-12015091	SK-N-SH	brain:	n/a	chr6:12014952-12014959 chr6:12014952-12014959 chr6:12014515-12014524 chr6:12014952-12014959
13	RCOR1	chr6:12012868-12015399	IMR90	lung:	n/a	n/a
14	POLR2A	chr6:12012455-12014736	HUVEC	blood vessel:	n/a	n/a
15	MAFK	chr6:12014080-12014852	Hela-S3	cervix:	n/a	chr6:12014101-12014116
16	POLR2A	chr6:12014083-12014875	MCF10A-Er-Src	breast:	n/a	n/a
17	ZNF143	chr6:12014143-12014567	K562	blood:	n/a	n/a
18	IRF1	chr6:12013400-12014876	K562	blood:	n/a	chr6:12013503-12013517 chr6:12013666-12013675
19	MAFK	chr6:12013945-12014277	HepG2	liver:	n/a	chr6:12014101-12014116
20	GATA3	chr6:12014095-12014922	MCF-7	breast:	n/a	chr6:12014515-12014524
21	EP300	chr6:12013380-12015010	Hela-S3	cervix:	n/a	chr6:12014549-12014558
22	POLR2A	chr6:12012840-12016065	GM12878	blood:	n/a	n/a
23	KAP1	chr6:12013886-12015820	K562	blood:	n/a	n/a
24	POLR2A	chr6:12007580-12016124	GM12878	blood:	n/a	n/a
25	GATA3	chr6:12014121-12014864	SK-N-SH	brain:	n/a	chr6:12014515-12014524
26	MXI1	chr6:12012983-12014307	GM12878	blood:	n/a	n/a
27	CUX1	chr6:12013442-12014776	K562	blood:	n/a	n/a
28	ZNF263	chr6:12012959-12014696	HEK293-T-REx	kidney:	n/a	chr6:12013384-12013393 chr6:12013433-12013454 chr6:12013381-12013390 chr6:12013370-12013391
29	CHD1	chr6:12008145-12015383	IMR90	lung:	n/a	chr6:12011541-12011551 chr6:12013007-12013017 chr6:12013336-12013346
30	REST	chr6:12012223-12014154	H1-neurons	neurons:	n/a	chr6:12013987-12013995 chr6:12012610-12012620 chr6:12012751-12012764 chr6:12012746-12012756
31	JUND	chr6:12013954-12014770	Hela-S3	cervix:	n/a	chr6:12014550-12014558 chr6:12014551-12014558 chr6:12014549-12014559 chr6:12014550-12014558
32	POLR2A	chr6:12011156-12014367	HUVEC	blood vessel:	n/a	n/a
33	ARID3A	chr6:12013373-12014695	K562	blood:	n/a	n/a
34	CHD1	chr6:12012951-12014309	GM12878	blood:	n/a	chr6:12013007-12013017 chr6:12013336-12013346
35	MAFF	chr6:12013343-12014249	HepG2	liver:	n/a	chr6:12014099-12014117
36	POLR2A	chr6:12008583-12014791	GM12878	blood:	n/a	n/a
37	CBX3	chr6:12014088-12015432	K562	blood:	n/a	n/a
38	POLR2A	chr6:12014114-12015678	GM12892	blood:	n/a	n/a
39	MAFK	chr6:12013286-12014849	IMR90	lung:	n/a	chr6:12013664-12013679 chr6:12014101-12014116
40	MAFK	chr6:12013397-12014311	HepG2	liver:	n/a	chr6:12013664-12013679 chr6:12014101-12014116
41	POLR2A	chr6:12008707-12014600	HUVEC	blood vessel:	n/a	n/a
42	STAT3	chr6:12013355-12014227	GM12878	blood:	n/a	chr6:12013601-12013612 chr6:12013597-12013617 chr6:12013597-12013617 chr6:12013432-12013444 chr6:12013658-12013665 chr6:12013603-12013611
43	RCOR1	chr6:12014133-12015195	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr6:12012922-12015356	GM12891	blood:	n/a	n/a
45	POLR2A	chr6:12008225-12014281	GM19099	blood:	n/a	n/a
46	MXI1	chr6:12010399-12014700	SK-N-SH	brain:	n/a	chr6:12011479-12011494
47	POLR2A	chr6:12008143-12014515	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr6:12012425-12014934	PFSK-1	brain:	n/a	n/a
49	RCOR1	chr6:12012989-12015179	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:11990522..11992970-chr6:12011349..12014154,2	MCF-7	breast:
2	chr6:12012948..12015001-chr6:12120385..12122503,2	K562	blood:
3	chr6:12012615..12014347-chr6:20401319..20403789,2	K562	blood:
4	chr6:11918788..11920525-chr6:12013699..12015737,2	K562	blood:
5	chr6:12009898..12015137-chr6:12286715..12292291,9	MCF-7	breast:
6	chr6:12013025..12015246-chr6:12052001..12053535,2	K562	blood:

Variant related genes	Relation type
HIVEP1	TF binding region
ENSG00000078401	Chromatin interaction
ENSG00000112242	Chromatin interaction
ENSG00000225102	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs16872190	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17486782	1.00[ASN][1000 genomes]
rs17676319	1.00[ASN][1000 genomes]
rs2024579	1.00[ASN][1000 genomes]
rs41273100	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55698720	1.00[ASN][1000 genomes]
rs55706944	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55718735	1.00[ASN][1000 genomes]
rs55760539	1.00[ASN][1000 genomes]
rs55797398	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55819840	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55839618	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55875423	1.00[ASN][1000 genomes]
rs55911725	1.00[ASN][1000 genomes]
rs55964029	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56050214	1.00[ASN][1000 genomes]
rs56087670	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56115353	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56138551	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56204496	1.00[ASN][1000 genomes]
rs56209525	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56294425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56321224	1.00[ASN][1000 genomes]
rs56412238	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56764416	1.00[ASN][1000 genomes]
rs57774273	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58026118	1.00[ASN][1000 genomes]
rs58086722	1.00[ASN][1000 genomes]
rs58221347	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59206097	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59592071	1.00[ASN][1000 genomes]
rs60200272	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60552066	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61227873	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62395405	1.00[ASN][1000 genomes]
rs6458056	1.00[ASN][1000 genomes]
rs66530314	1.00[ASN][1000 genomes]
rs66614912	1.00[ASN][1000 genomes]
rs66708680	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66720565	1.00[ASN][1000 genomes]
rs66727286	1.00[ASN][1000 genomes]
rs66964129	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67170588	1.00[ASN][1000 genomes]
rs67757013	1.00[ASN][1000 genomes]
rs67843209	1.00[ASN][1000 genomes]
rs68009879	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68019130	1.00[ASN][1000 genomes]
rs6916070	1.00[ASN][1000 genomes]
rs72826009	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826011	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826025	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826027	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826092	1.00[ASN][1000 genomes]
rs72828105	1.00[ASN][1000 genomes]
rs742750	1.00[ASN][1000 genomes]
rs876829	1.00[ASN][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	nsv970323	chr6:12006884-12020375	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv3327745	chr6:12011191-12014339	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12008400-12014200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:12008600-12014200	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr6:12008600-12014400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:12008600-12014400	Active TSS	Aorta	Aorta
5	chr6:12008800-12014400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:12010600-12014200	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr6:12010600-12014400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:12010800-12014200	Active TSS	H1 Cell Line	embryonic stem cell
9	chr6:12010800-12014200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr6:12010800-12014200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:12010800-12014400	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr6:12011000-12014600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:12011000-12014600	Active TSS	HSMMtube	muscle
14	chr6:12011200-12014600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:12011200-12014600	Active TSS	Fetal Brain Female	brain
16	chr6:12011400-12014200	Active TSS	Fetal Intestine Large	intestine
17	chr6:12012200-12014600	Active TSS	GM12878-XiMat	blood
18	chr6:12012600-12014200	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr6:12012600-12014200	Active TSS	A549	lung
20	chr6:12013000-12014200	Active TSS	Fetal Brain Male	brain
21	chr6:12013400-12014200	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr6:12013400-12014200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:12013400-12014200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:12013400-12014200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr6:12013400-12014400	Flanking Active TSS	K562	blood
26	chr6:12013400-12014600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:12013400-12014800	Active TSS	Brain Germinal Matrix	brain
28	chr6:12013600-12014200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr6:12013600-12014200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr6:12013600-12014200	Flanking Active TSS	Fetal Heart	heart
31	chr6:12013600-12014200	Active TSS	Right Atrium	heart
32	chr6:12013600-12014200	Flanking Active TSS	Hela-S3	cervix
33	chr6:12013600-12014400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:12013600-12014400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:12013600-12014400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr6:12013600-12014400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:12013600-12014400	Flanking Active TSS	Liver	Liver
38	chr6:12013600-12014400	Flanking Active TSS	HMEC	breast
39	chr6:12013600-12014400	Flanking Active TSS	NH-A	brain
40	chr6:12013600-12014400	Flanking Active TSS	Osteobl	bone
41	chr6:12013600-12014600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:12013600-12015000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:12013600-12015200	Flanking Active TSS	HUVEC	blood vessel
44	chr6:12013800-12014200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr6:12013800-12014200	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr6:12013800-12014200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr6:12013800-12014200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:12013800-12014200	Flanking Active TSS	Fetal Kidney	kidney
49	chr6:12013800-12014200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr6:12013800-12014400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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