Variant report

Variant	rs56045105
Chromosome Location	chr6:29595015-29595016
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:122)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:29595000-29595150	HCPEpiC	choroid plexus:	n/a	n/a
2	POLR2A	chr6:29594652-29596964	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr6:29594328-29597108	K562	blood:	n/a	n/a
4	SIN3A	chr6:29594691-29597089	H1-hESC	embryonic stem cell:	n/a	n/a
5	ZBTB7A	chr6:29594871-29597108	K562	blood:	n/a	chr6:29595188-29595197 chr6:29595689-29595698
6	POLR2A	chr6:29594861-29597047	K562	blood:	n/a	n/a
7	CHD2	chr6:29594791-29595113	K562	blood:	n/a	n/a
8	POLR2A	chr6:29594210-29596810	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr6:29594744-29596971	K562	blood:	n/a	n/a
10	POLR2A	chr6:29593077-29597878	K562	blood:	n/a	n/a
11	REST	chr6:29594215-29597204	H1-neurons	neurons:	n/a	chr6:29596563-29596573
12	MAZ	chr6:29594519-29597214	IMR90	lung:	n/a	chr6:29595569-29595578 chr6:29594847-29594856 chr6:29595685-29595695
13	ZBTB7A	chr6:29594873-29596768	K562	blood:	n/a	chr6:29595188-29595197 chr6:29595689-29595698

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:29595011-29595061	A549	lung:	n/a
2	chr6:29595011-29595061	SKMC	muscle:	n/a
3	chr6:29595002-29595052	HRE	kidney:	n/a
4	chr6:29595002-29595052	HEK293	kidney:	embryo
5	chr6:29595002-29595052	GM12891	blood:	n/a
6	chr6:29595011-29595061	NB4	blood:	n/a
7	chr6:29595011-29595061	NH-A	brain:	n/a
8	chr6:29595011-29595061	NT2-D1	testis:	n/a
9	chr6:29595002-29595052	IMR90	lung:	fetal
10	chr6:29595011-29595061	NHBE	bronchial:	n/a
11	chr6:29595011-29595061	BE2_C	brain:	n/a
12	chr6:29595011-29595061	GM19239	blood:	n/a
13	chr6:29595002-29595052	A549	lung:	n/a
14	chr6:29595011-29595061	Hepatocyte	liver:	n/a
15	chr6:29595011-29595061	HAEpiC	amniotic membrane:	n/a
16	chr6:29595002-29595052	HUVEC	blood vessel:	n/a
17	chr6:29595002-29595052	GM12892	blood:	n/a
18	chr6:29595011-29595061	ProgFib	skin:	n/a
19	chr6:29595002-29595052	BE2_C	brain:	n/a
20	chr6:29595011-29595061	MCF10A-Er-Src	breast:	n/a
21	chr6:29595011-29595061	HPAEpiC	pulmonary alveolar:	n/a
22	chr6:29595002-29595052	Hepatocyte	liver:	n/a
23	chr6:29595011-29595061	HEK293	kidney:	embryo
24	chr6:29595002-29595052	HL-60	blood:	n/a
25	chr6:29595002-29595052	HRPEpiC	eye:	n/a
26	chr6:29595011-29595061	HUVEC	blood vessel:	n/a
27	chr6:29595002-29595052	MCF10A-Er-Src	breast:	n/a
28	chr6:29595011-29595061	Jurkat	blood:	n/a
29	chr6:29595002-29595052	AG04450	lung:	fetal
30	chr6:29595002-29595052	T-47D	breast:	n/a
31	chr6:29595011-29595061	HRPEpiC	eye:	n/a
32	chr6:29595011-29595061	RPTEC	kidney:	n/a
33	chr6:29595002-29595052	MCF-7	breast:	n/a
34	chr6:29595002-29595052	HAEpiC	amniotic membrane:	n/a
35	chr6:29595002-29595052	HCM	heart:	n/a
36	chr6:29595002-29595052	NB4	blood:	n/a
37	chr6:29595002-29595052	PrEC	prostate:	n/a
38	chr6:29595002-29595052	ovcar-3	ovarian:	n/a
39	chr6:29595002-29595052	K562	blood:	n/a
40	chr6:29595002-29595052	AoSMC	blood vessel:	n/a
41	chr6:29595011-29595061	SK-N-MC	brain:	n/a
42	chr6:29595011-29595061	K562	blood:	n/a
43	chr6:29595011-29595061	CMK	blood:	n/a
44	chr6:29595011-29595061	Caco-2	colon:	n/a
45	chr6:29595011-29595061	GM06990	blood:	n/a
46	chr6:29595002-29595052	PFSK-1	brain:	n/a
47	chr6:29595011-29595061	ovcar-3	ovarian:	n/a
48	chr6:29595002-29595052	GM12878	blood:	n/a
49	chr6:29595002-29595052	U87	brain:	n/a
50	chr6:29595002-29595052	BJ	skin:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:29579403..29583874-chr6:29593619..29596165,4	K562	blood:
2	chr6:29588563..29590389-chr6:29593488..29595808,2	MCF-7	breast:
3	chr6:29576473..29579282-chr6:29593372..29595835,2	K562	blood:
4	chr6:29590884..29592838-chr6:29594081..29596574,2	MCF-7	breast:
5	chr6:29564780..29575712-chr6:29592511..29597522,14	K562	blood:
6	chr6:29572757..29580903-chr6:29593317..29599166,10	K562	blood:
7	chr6:28975781..28978716-chr6:29592813..29595617,2	K562	blood:

No data

Variant related genes	Relation type
GABBR1	TF binding region
GABBR1	CpG island
ENSG00000204681	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs16895101	0.94[ASN][1000 genomes]
rs16895218	0.82[AMR][1000 genomes]
rs2057010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2058325	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2058326	0.83[ASN][1000 genomes]
rs28359971	0.85[ASN][1000 genomes]
rs28359972	0.87[ASN][1000 genomes]
rs28749524	0.87[ASN][1000 genomes]
rs29219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29233	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs29254	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs29256	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs29266	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3025628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3025642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs362515	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs362517	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55701059	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55871431	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55888673	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55971964	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56020557	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56106029	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56142919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56155438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56393713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62392941	0.96[ASN][1000 genomes]
rs62392942	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62392943	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62392944	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62392946	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62406580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62406582	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62406583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406584	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72831507	0.94[EUR][1000 genomes];0.91[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	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29566400-29595200	Weak transcription	Right Atrium	heart
2	chr6:29567600-29595400	Weak transcription	A549	lung
3	chr6:29568600-29595200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:29569400-29595600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:29572200-29595600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr6:29574400-29595400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:29577600-29595400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:29578800-29595200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:29581800-29596000	Weak transcription	Fetal Heart	heart
10	chr6:29582600-29595400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:29589200-29595200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:29589200-29595400	Weak transcription	NHDF-Ad	bronchial
13	chr6:29589200-29595600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:29589400-29595400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr6:29589400-29595400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:29589400-29595400	Weak transcription	HSMM	muscle
17	chr6:29590200-29595200	Weak transcription	Fetal Kidney	kidney
18	chr6:29590200-29595400	Weak transcription	Esophagus	oesophagus
19	chr6:29590800-29595200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr6:29591200-29595200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr6:29591400-29595400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr6:29591600-29595200	Weak transcription	Lung	lung
23	chr6:29591600-29595400	Weak transcription	Aorta	Aorta
24	chr6:29591600-29595400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr6:29591600-29595600	Weak transcription	Gastric	stomach
26	chr6:29591800-29595200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr6:29591800-29595400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:29591800-29595600	Weak transcription	Spleen	Spleen
29	chr6:29591800-29595600	Weak transcription	Dnd41	blood
30	chr6:29591800-29595600	Weak transcription	HMEC	breast
31	chr6:29592000-29595200	Weak transcription	Colonic Mucosa	Colon
32	chr6:29592000-29595200	Weak transcription	Right Ventricle	heart
33	chr6:29592000-29595400	Weak transcription	Adipose Nuclei	Adipose
34	chr6:29592200-29595400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:29592200-29595400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr6:29592200-29596000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:29592200-29596400	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr6:29592800-29595200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
39	chr6:29592800-29595200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:29592800-29595600	Weak transcription	NHEK	skin
41	chr6:29593000-29595200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:29593000-29596600	Active TSS	Brain Cingulate Gyrus	brain
43	chr6:29593200-29596200	Active TSS	Brain Anterior Caudate	brain
44	chr6:29593200-29596400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:29593400-29595600	Weak transcription	Fetal Lung	lung
46	chr6:29593400-29596200	Active TSS	Brain Substantia Nigra	brain
47	chr6:29593600-29598200	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr6:29593800-29596600	Active TSS	Brain Angular Gyrus	brain
49	chr6:29594000-29596200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr6:29594200-29595200	Flanking Active TSS	H1 Cell Line	embryonic stem cell

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