Variant report

Variant	rs73348609
Chromosome Location	chr6:2449023-2449024
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	RAD21	chr6:2448951-2449405	Hela-S3	cervix:	n/a	chr6:2449162-2449181
2	ZNF384	chr6:2448977-2449328	K562	blood:	n/a	n/a
3	RAD21	chr6:2448915-2449324	SK-N-SH_RA	brain:	n/a	chr6:2449162-2449181
4	RAD21	chr6:2448782-2449546	HCT-116	colon:	n/a	chr6:2449162-2449181
5	RAD21	chr6:2448842-2449470	A549	lung:	n/a	chr6:2449162-2449181
6	CTCF	chr6:2449020-2449170	GM12866	blood:	n/a	n/a
7	RAD21	chr6:2448775-2449503	IMR90	lung:	n/a	chr6:2449162-2449181
8	RAD21	chr6:2448954-2449364	HepG2	liver:	n/a	chr6:2449162-2449181
9	CTCF	chr6:2448980-2449373	GM12878	blood:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180
10	CTCF	chr6:2449000-2449150	HFF	foreskin:	n/a	n/a
11	CTCF	chr6:2449019-2449320	HUVEC	blood vessel:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180
12	RAD21	chr6:2448956-2449273	GM12878	blood:	n/a	chr6:2449162-2449181
13	RAD21	chr6:2448700-2449603	HCT-116	colon:	n/a	chr6:2449162-2449181
14	RAD21	chr6:2448911-2449487	MCF-7	breast:	n/a	chr6:2449162-2449181
15	CTCF	chr6:2448945-2449433	IMR90	lung:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180
16	RAD21	chr6:2448542-2449748	SK-N-SH	brain:	n/a	chr6:2449162-2449181
17	CTCF	chr6:2448936-2449366	K562	blood:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180
18	CREB1	chr6:2448918-2449648	H1-hESC	embryonic stem cell:	n/a	chr6:2449417-2449430 chr6:2449417-2449430
19	TCF12	chr6:2448922-2449564	A549	lung:	n/a	n/a
20	SMC3	chr6:2448974-2449428	Hela-S3	cervix:	n/a	n/a
21	RAD21	chr6:2448965-2449337	GM12878	blood:	n/a	chr6:2449162-2449181
22	ZNF143	chr6:2449012-2449350	K562	blood:	n/a	n/a
23	CTCF	chr6:2449009-2449350	T-47D	breast:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180
24	SMC3	chr6:2448979-2449356	GM12878	blood:	n/a	n/a
25	CTCF	chr6:2448978-2449356	ECC-1	luminal epithelium:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180
26	CTCF	chr6:2449000-2449150	HMEC	breast:	n/a	n/a
27	MYC	chr6:2449023-2449365	NB4	blood:	n/a	n/a
28	MAX	chr6:2448948-2449572	A549	lung:	n/a	n/a
29	CTCF	chr6:2449020-2449170	HCM	heart:	n/a	n/a
30	CTCF	chr6:2448915-2449536	HCT-116	colon:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180
31	CTCF	chr6:2448940-2449090	GM12870	blood:	n/a	n/a
32	CTCF	chr6:2449000-2449150	HFF-Myc	foreskin:	n/a	n/a
33	CTCF	chr6:2448743-2449397	K562	blood:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180
34	CTCF	chr6:2449015-2449265	SK-N-SH_RA	brain:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180
35	BRCA1	chr6:2449010-2449416	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr6:2448973-2449420	MCF-7	breast:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180
37	SMC3	chr6:2448943-2449351	HepG2	liver:	n/a	n/a
38	CTCF	chr6:2448871-2449560	HCT-116	colon:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180
39	SMC3	chr6:2448993-2449333	K562	blood:	n/a	n/a
40	RAD21	chr6:2448947-2449443	H1-hESC	embryonic stem cell:	n/a	chr6:2449162-2449181
41	RAD21	chr6:2448953-2449409	H1-hESC	embryonic stem cell:	n/a	chr6:2449162-2449181
42	ZNF384	chr6:2448997-2449274	GM12878	blood:	n/a	n/a
43	CTCF	chr6:2448773-2449590	A549	lung:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180
44	RAD21	chr6:2448864-2449472	MCF-7	breast:	n/a	chr6:2449162-2449181
45	CTCF	chr6:2448968-2449396	H1-hESC	embryonic stem cell:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180
46	CTCF	chr6:2449016-2449317	Medullo	brain:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180
47	ATF2	chr6:2448968-2449569	H1-hESC	embryonic stem cell:	n/a	n/a
48	RAD21	chr6:2448892-2449384	A549	lung:	n/a	chr6:2449162-2449181
49	SPI1	chr6:2448975-2449570	HL-60	blood:	n/a	chr6:2449373-2449382 chr6:2449542-2449549
50	CTCF	chr6:2449018-2449361	H1-hESC	embryonic stem cell:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180

No.	Distal block	Cell Line	Cell type
1	chr6:1596198..1597096-chr6:2448736..2449270,3	K562	blood:
2	chr6:2353810..2354693-chr6:2448790..2449627,3	MCF-7	breast:
3	chr6:2209266..2210149-chr6:2448969..2449652,2	MCF-7	breast:
4	chr6:2448902..2449578-chr6:2695787..2696287,2	MCF-7	breast:
5	chr6:2448825..2449584-chr6:2634344..2635312,4	MCF-7	breast:
6	chr6:2448317..2449241-chr6:2484813..2485374,2	K562	blood:

Variant related genes	Relation type
GMDS-AS1	TF binding region
ENSG00000164385	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11964241	0.87[AMR][1000 genomes]
rs28633763	0.87[AMR][1000 genomes]
rs4602753	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57908018	1.00[AMR][1000 genomes]
rs59455919	0.87[AMR][1000 genomes]
rs60798809	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6901457	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6904942	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6905100	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6905118	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6909863	1.00[AMR][1000 genomes]
rs6929207	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73344778	0.87[AMR][1000 genomes]
rs73344794	0.87[AMR][1000 genomes]
rs73344796	0.87[AMR][1000 genomes]
rs73346609	0.87[AMR][1000 genomes]
rs73346610	0.87[AMR][1000 genomes]
rs73346620	0.87[AMR][1000 genomes]
rs73346662	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73346668	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73346669	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73346702	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7739140	0.87[AMR][1000 genomes]
rs7744661	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
2	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
5	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
6	nsv883390	chr6:2265344-2584919	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv883391	chr6:2282747-2507448	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1016878	chr6:2375784-2680476	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv498004	chr6:2380300-3313587	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	163 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2399800-2449200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr6:2402200-2449200	Weak transcription	Left Ventricle	heart
3	chr6:2414600-2452000	Weak transcription	Ovary	ovary
4	chr6:2414800-2449200	Weak transcription	Fetal Stomach	stomach
5	chr6:2417600-2454200	Weak transcription	Pancreas	Pancrea
6	chr6:2432200-2449200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:2433200-2449200	Weak transcription	Adipose Nuclei	Adipose
8	chr6:2434400-2449200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:2435000-2449200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:2435400-2449200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:2438800-2449400	Weak transcription	Primary T cells from cord blood	blood
12	chr6:2440200-2449200	Weak transcription	Aorta	Aorta
13	chr6:2442600-2449200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:2443000-2449200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:2444000-2449200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:2444400-2449200	Weak transcription	Brain Hippocampus Middle	brain
17	chr6:2447000-2449200	Enhancers	Fetal Intestine Small	intestine
18	chr6:2447600-2449400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:2447800-2449200	Enhancers	Fetal Intestine Large	intestine
20	chr6:2447800-2449200	Enhancers	Fetal Lung	lung
21	chr6:2447800-2449200	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr6:2448000-2449200	Enhancers	Fetal Kidney	kidney
23	chr6:2448000-2449200	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr6:2448000-2449200	Weak transcription	HepG2	liver
25	chr6:2448200-2449200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:2448200-2449200	Enhancers	Osteobl	bone
27	chr6:2448400-2449200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:2448400-2449200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:2448400-2449200	Enhancers	NHDF-Ad	bronchial
30	chr6:2448400-2450000	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr6:2448600-2449200	Enhancers	Brain Anterior Caudate	brain
32	chr6:2448600-2449200	Enhancers	Fetal Heart	heart
33	chr6:2448600-2449200	Enhancers	HUVEC	blood vessel
34	chr6:2448600-2449600	Enhancers	Duodenum Mucosa	Duodenum
35	chr6:2448600-2449800	Enhancers	Fetal Brain Male	brain
36	chr6:2448600-2451400	Enhancers	Hela-S3	cervix
37	chr6:2448800-2449200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:2448800-2450000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:2449000-2449200	Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr6:2449000-2449200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr6:2449000-2449200	Enhancers	HMEC	breast
42	chr6:2449000-2449400	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr6:2449000-2449400	Active TSS	Brain Germinal Matrix	brain
44	chr6:2449000-2449600	Active TSS	Brain Angular Gyrus	brain

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