Variant report

Variant	rs73738742
Chromosome Location	chr6:27280095-27280096
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	BRCA1	chr6:27280025-27280189	GM12878	blood:	n/a	n/a
2	MAX	chr6:27279507-27280190	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr6:27280040-27280288	GM12878	blood:	n/a	n/a
4	MAX	chr6:27279479-27280881	A549	lung:	n/a	n/a
5	CTCF	chr6:27280020-27280170	SAEC	small airway:	n/a	n/a
6	SMC3	chr6:27279813-27280962	SK-N-SH	brain:	n/a	chr6:27280635-27280649
7	CTCF	chr6:27279960-27280110	NHEK	skin:	n/a	n/a
8	YY1	chr6:27279985-27280325	GM12878	blood:	n/a	n/a
9	RAD21	chr6:27280048-27280854	IMR90	lung:	n/a	chr6:27280634-27280653
10	ELF1	chr6:27279673-27280871	GM12878	blood:	n/a	chr6:27280597-27280608
11	RUNX3	chr6:27280036-27280795	GM12878	blood:	n/a	n/a
12	ZBTB33	chr6:27279910-27280229	GM12878	blood:	n/a	n/a
13	SMC3	chr6:27280089-27280913	GM12878	blood:	n/a	chr6:27280635-27280649
14	CTCF	chr6:27280090-27280108	Fibrobl	skin:	n/a	n/a
15	RCOR1	chr6:27280040-27280866	GM12878	blood:	n/a	n/a
16	CTCF	chr6:27280020-27280170	HVMF	connective:	n/a	n/a
17	CTCF	chr6:27280084-27280426	GM19239	blood:	n/a	n/a
18	POLR2A	chr6:27280077-27280357	MCF-7	breast:	n/a	n/a
19	CTCF	chr6:27280036-27280912	GM12878	blood:	n/a	chr6:27280633-27280651 chr6:27280635-27280656
20	CTCF	chr6:27280000-27280150	GM12868	blood:	n/a	n/a
21	E2F6	chr6:27279351-27280833	H1-hESC	embryonic stem cell:	n/a	n/a
22	MYC	chr6:27279600-27280114	H1-hESC	embryonic stem cell:	n/a	n/a
23	RAD21	chr6:27279554-27280893	H1-hESC	embryonic stem cell:	n/a	chr6:27280634-27280653
24	CTCF	chr6:27280020-27280170	BE2_C	brain:	n/a	n/a
25	CTCF	chr6:27280080-27280230	HCM	heart:	n/a	n/a
26	SIN3A	chr6:27279775-27280838	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr6:27280093-27280836	IMR90	lung:	n/a	chr6:27280633-27280651 chr6:27280635-27280656
28	E2F6	chr6:27279160-27280852	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr6:27280074-27280373	GM12892	blood:	n/a	n/a
30	ELF1	chr6:27280053-27280836	GM12878	blood:	n/a	chr6:27280597-27280608
31	CHD2	chr6:27279689-27280725	H1-hESC	embryonic stem cell:	n/a	chr6:27280236-27280246 chr6:27280271-27280281
32	CTCF	chr6:27280079-27280355	GM19238	blood:	n/a	n/a
33	CTCF	chr6:27280080-27280230	GM12866	blood:	n/a	n/a
34	CTCF	chr6:27280012-27280992	MCF-7	breast:	n/a	chr6:27280633-27280651 chr6:27280635-27280656
35	MAX	chr6:27279678-27280859	A549	lung:	n/a	n/a
36	CTCF	chr6:27279844-27281161	A549	lung:	n/a	chr6:27280633-27280651 chr6:27280635-27280656
37	MAX	chr6:27279457-27280837	H1-hESC	embryonic stem cell:	n/a	n/a
38	CHD2	chr6:27280087-27280750	GM12878	blood:	n/a	chr6:27280236-27280246 chr6:27280271-27280281
39	RAD21	chr6:27279953-27281063	SK-N-SH	brain:	n/a	chr6:27280634-27280653
40	SPI1	chr6:27280027-27280789	HL-60	blood:	n/a	chr6:27280256-27280263
41	BACH1	chr6:27279940-27280953	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr6:27280057-27280809	GM12891	blood:	n/a	chr6:27280633-27280651 chr6:27280635-27280656
43	CTCF	chr6:27279960-27280110	HCM	heart:	n/a	n/a
44	CTCF	chr6:27280060-27280210	WERI-Rb-1	eye:	n/a	n/a
45	MAX	chr6:27279426-27280863	H1-hESC	embryonic stem cell:	n/a	n/a
46	RAD21	chr6:27279877-27280900	H1-hESC	embryonic stem cell:	n/a	chr6:27280634-27280653
47	CTCF	chr6:27279876-27281039	SK-N-SH	brain:	n/a	chr6:27280633-27280651 chr6:27280635-27280656
48	MAX	chr6:27280059-27280888	ECC-1	luminal epithelium:	n/a	n/a
49	E2F6	chr6:27279630-27280796	A549	lung:	n/a	n/a
50	CTCF	chr6:27280060-27280210	GM12870	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27279187..27280995-chr6:27439360..27441808,2	MCF-7	breast:
2	chr6:27114741..27116846-chr6:27278241..27280578,2	K562	blood:

Variant related genes	Relation type
POM121L2	TF binding region
ENSG00000184825	Chromatin interaction
ENSG00000096654	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs28542968	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61736094	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61736098	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61743942	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61743950	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61746402	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9461346	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9461347	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9461348	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9461349	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9461350	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9461351	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9461352	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9461354	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468028	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468029	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468030	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468036	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468037	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468038	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468039	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468040	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468041	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468042	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468043	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468045	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9468046	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468047	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468050	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468055	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468056	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468057	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9468059	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468061	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468062	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468063	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9468066	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs956149	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs956150	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv883505	chr6:27210614-27300580	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv883506	chr6:27271343-27288687	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv883507	chr6:27279982-27318836	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 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	chr6:27279400-27280600	Active TSS	Gastric	stomach
2	chr6:27279400-27281000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr6:27279400-27281000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:27279400-27281000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
5	chr6:27279400-27281000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:27279600-27280200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:27279600-27280200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
8	chr6:27279600-27280200	Enhancers	Spleen	Spleen
9	chr6:27279600-27280400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
10	chr6:27279600-27280600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
11	chr6:27279600-27280600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:27279600-27280800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:27279600-27280800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr6:27279600-27280800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:27279600-27281000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr6:27279600-27281000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
17	chr6:27279600-27281000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:27279800-27280200	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:27279800-27280200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:27279800-27280200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:27279800-27280200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:27279800-27280200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
23	chr6:27279800-27280200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
24	chr6:27279800-27280200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
25	chr6:27279800-27280200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:27279800-27280200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
27	chr6:27279800-27280200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
28	chr6:27279800-27280200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
29	chr6:27279800-27280200	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas
30	chr6:27279800-27280200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
31	chr6:27279800-27280200	Flanking Bivalent TSS/Enh	Thymus	Thymus
32	chr6:27279800-27280200	Flanking Active TSS	GM12878-XiMat	blood
33	chr6:27279800-27280400	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:27279800-27280400	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:27279800-27280400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
36	chr6:27279800-27280400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
37	chr6:27279800-27280400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:27279800-27280400	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
39	chr6:27279800-27280400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
40	chr6:27279800-27280400	Bivalent Enhancer	Fetal Brain Male	brain
41	chr6:27279800-27280400	Flanking Active TSS	Right Atrium	heart
42	chr6:27279800-27280600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr6:27279800-27280600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr6:27279800-27280600	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:27279800-27280600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:27279800-27280600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr6:27279800-27280600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
48	chr6:27279800-27280600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
49	chr6:27279800-27280600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
50	chr6:27279800-27280600	Flanking Bivalent TSS/Enh	HUVEC	blood vessel

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