Variant report

Variant	rs71566478
Chromosome Location	chr6:147827880-147827881
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	CTCF	chr6:147827760-147827910	HAc	cerebellar:	n/a	n/a
2	CTCF	chr6:147827809-147828068	GM19240	blood:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
3	ZMIZ1	chr6:147827789-147827989	K562	blood:	n/a	n/a
4	CTCF	chr6:147827820-147827970	GM12872	blood:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
5	CTCF	chr6:147827800-147827950	K562	blood:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
6	CTCF	chr6:147827741-147828081	K562	blood:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
7	CTCF	chr6:147827717-147827992	A549	lung:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
8	CTCF	chr6:147827880-147828030	Caco-2	colon:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
9	CTCF	chr6:147827820-147827970	GM12864	blood:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
10	CTCF	chr6:147827840-147827990	HAc	cerebellar:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
11	CTCF	chr6:147827820-147827970	GM12878	blood:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
12	CTCF	chr6:147827804-147828052	Lung_OC	lung:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
13	RAD21	chr6:147827554-147828344	HCT-116	colon:	n/a	chr6:147827919-147827938 chr6:147828092-147828106
14	CCNT2	chr6:147827843-147828115	K562	blood:	n/a	n/a
15	YY1	chr6:147827825-147828116	K562	blood:	n/a	n/a
16	CTCF	chr6:147827860-147828010	GM12869	blood:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
17	CTCF	chr6:147827860-147828010	GM12864	blood:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
18	RAD21	chr6:147827681-147828388	ECC-1	luminal epithelium:	n/a	chr6:147827919-147827938 chr6:147828092-147828106
19	CTCF	chr6:147827760-147827910	NHEK	skin:	n/a	n/a
20	CTCF	chr6:147827840-147827990	HCFaa	heart:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
21	CTCF	chr6:147827860-147828010	GM12874	blood:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
22	RAD21	chr6:147827676-147828220	ECC-1	luminal epithelium:	n/a	chr6:147827919-147827938 chr6:147828092-147828106
23	CTCF	chr6:147827789-147827996	A549	lung:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
24	CTCF	chr6:147827820-147827970	AG09319	gingival:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
25	CTBP2	chr6:147827814-147828813	H1-hESC	embryonic stem cell:	n/a	n/a
26	RAD21	chr6:147827733-147828129	K562	blood:	n/a	chr6:147827919-147827938 chr6:147828092-147828106
27	RAD21	chr6:147827698-147828254	IMR90	lung:	n/a	chr6:147827919-147827938 chr6:147828092-147828106
28	YY1	chr6:147827830-147827958	K562	blood:	n/a	n/a
29	CTCF	chr6:147827860-147828010	HepG2	liver:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
30	YY1	chr6:147827834-147828080	GM12878	blood:	n/a	n/a
31	RAD21	chr6:147827792-147828123	SK-N-SH_RA	brain:	n/a	chr6:147827919-147827938 chr6:147828092-147828106
32	CTCF	chr6:147827805-147828044	HepG2	liver:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
33	CTCF	chr6:147827860-147828010	AG04449	skin:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
34	FOXP2	chr6:147827847-147828158	PFSK-1	brain:	n/a	n/a
35	CTCF	chr6:147827880-147828030	GM12866	blood:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
36	CTCF	chr6:147827800-147827950	HPAF	blood vessel:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
37	CTCF	chr6:147827727-147828128	K562	blood:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
38	CTCF	chr6:147827860-147828010	GM12865	blood:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
39	RAD21	chr6:147827631-147828348	SK-N-SH	brain:	n/a	chr6:147827919-147827938 chr6:147828092-147828106
40	CTCF	chr6:147827840-147827990	WERI-Rb-1	eye:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
41	ZNF143	chr6:147827815-147828084	GM12878	blood:	n/a	n/a
42	CTCF	chr6:147827819-147828100	T-47D	breast:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
43	CTCF	chr6:147827840-147827990	HEK293	kidney:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
44	CTCF	chr6:147827840-147827990	HRE	kidney:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
45	RAD21	chr6:147827733-147828111	SK-N-SH_RA	brain:	n/a	chr6:147827919-147827938 chr6:147828092-147828106
46	CTCF	chr6:147827772-147828063	LNCaP	prostate:	n/a	chr6:147827918-147827936 chr6:147827919-147827935
47	RAD21	chr6:147827713-147828149	HepG2	liver:	n/a	chr6:147827919-147827938 chr6:147828092-147828106
48	CUX1	chr6:147827771-147827893	K562	blood:	n/a	n/a
49	CHD2	chr6:147827878-147828139	K562	blood:	n/a	n/a
50	CTCF	chr6:147827786-147828064	ProgFib	skin:	n/a	chr6:147827918-147827936 chr6:147827919-147827935

No.	Distal block	Cell Line	Cell type
1	chr6:147827833..147828480-chr6:148785570..148786546,4	K562	blood:
2	chr6:147827401..147828161-chr6:148487222..148488157,2	K562	blood:
3	chr6:147827861..147828432-chr6:148500915..148501627,3	K562	blood:

Variant related genes	Relation type
SAMD5	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10499248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13205501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13207751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13210148	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13211031	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13211278	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13214443	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13218201	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13220031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13220208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17076897	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34358483	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34790023	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35009077	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35506695	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35658484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35987208	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574551	1.00[AFR][1000 genomes]
rs599429	1.00[AFR][1000 genomes]
rs71547193	0.81[AMR][1000 genomes]
rs71566479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9688849	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9689689	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:147827600-147828000	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
2	chr6:147827800-147828000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:147827800-147828000	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:147827800-147828000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:147827800-147828000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:147827800-147828000	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
7	chr6:147827800-147828000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:147827800-147828000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:147827800-147828000	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:147827800-147828000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:147827800-147828000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:147827800-147828000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:147827800-147828000	Active TSS	Brain Angular Gyrus	brain
14	chr6:147827800-147828000	Flanking Active TSS	Brain Cingulate Gyrus	brain
15	chr6:147827800-147828000	Active TSS	Brain Germinal Matrix	brain
16	chr6:147827800-147828000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
17	chr6:147827800-147828000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:147827800-147828000	Active TSS	Brain Substantia Nigra	brain
19	chr6:147827800-147828000	Enhancers	Colonic Mucosa	Colon
20	chr6:147827800-147828000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
21	chr6:147827800-147828000	Active TSS	Fetal Intestine Large	intestine
22	chr6:147827800-147828000	Active TSS	Fetal Intestine Small	intestine
23	chr6:147827800-147828000	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
24	chr6:147827800-147828000	Active TSS	Fetal Stomach	stomach
25	chr6:147827800-147828000	Enhancers	Gastric	stomach
26	chr6:147827800-147828000	Enhancers	Lung	lung
27	chr6:147827800-147828000	Active TSS	Ovary	ovary
28	chr6:147827800-147828000	Enhancers	Pancreas	Pancrea
29	chr6:147827800-147828000	Enhancers	Placenta Amnion	Placenta Amnion
30	chr6:147827800-147828000	Bivalent/Poised TSS	Psoas Muscle	Psoas
31	chr6:147827800-147828000	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr6:147827800-147828000	Active TSS	Rectal Mucosa Donor 31	rectum
33	chr6:147827800-147828000	Genic enhancers	Right Atrium	heart
34	chr6:147827800-147828000	Active TSS	Right Ventricle	heart
35	chr6:147827800-147828000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
36	chr6:147827800-147828000	Bivalent Enhancer	HepG2	liver
37	chr6:147827800-147828000	Enhancers	HSMMtube	muscle
38	chr6:147827800-147828000	Active TSS	HUVEC	blood vessel
39	chr6:147827800-147828000	Enhancers	NHDF-Ad	bronchial
40	chr6:147827800-147828000	Bivalent/Poised TSS	NHEK	skin
41	chr6:147827800-147828000	Active TSS	NHLF	lung
42	chr6:147827800-147828200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:147827800-147828200	Active TSS	Brain Anterior Caudate	brain
44	chr6:147827800-147828200	Flanking Active TSS	Fetal Brain Male	brain
45	chr6:147827800-147828200	Bivalent/Poised TSS	Fetal Brain Female	brain
46	chr6:147827800-147828400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:147827800-147828400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr6:147827800-147828400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr6:147827800-147828400	Flanking Active TSS	Fetal Kidney	kidney
50	chr6:147827800-147828400	Flanking Active TSS	HMEC	breast

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