Variant report

Variant	rs3025628
Chromosome Location	chr6:29590349-29590350
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	ZNF143	chr6:29590317-29590409	H1-hESC	embryonic stem cell:	n/a	n/a
2	BATF	chr6:29590264-29590467	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29589009..29590540-chr6:29598383..29601313,2	MCF-7	breast:
2	chr6:29578000..29583607-chr6:29584816..29592316,14	K562	blood:

Variant related genes	Relation type
GABBR1	TF binding region
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]
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]
rs56045105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:110 , 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	chr6:29566800-29590600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:29567600-29592400	Strong transcription	Fetal Stomach	stomach
4	chr6:29567600-29595400	Weak transcription	A549	lung
5	chr6:29568600-29595200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:29569000-29592400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:29569200-29592200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:29569400-29592000	Strong transcription	Stomach Smooth Muscle	stomach
9	chr6:29569400-29595600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:29572200-29595600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:29572400-29592000	Strong transcription	Fetal Brain Female	brain
12	chr6:29572400-29593000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:29573000-29591000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr6:29574400-29595400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:29574800-29595000	Weak transcription	Pancreas	Pancrea
16	chr6:29575200-29590800	Weak transcription	Primary T cells from cord blood	blood
17	chr6:29575400-29591600	Weak transcription	Colonic Mucosa	Colon
18	chr6:29577000-29591600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr6:29577600-29595400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:29578800-29595200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr6:29580400-29592200	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr6:29581200-29591600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:29581800-29596000	Weak transcription	Fetal Heart	heart
24	chr6:29582600-29595400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr6:29583800-29592200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:29585400-29591400	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr6:29585400-29591600	Strong transcription	K562	blood
28	chr6:29585400-29591800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr6:29585400-29591800	Strong transcription	NH-A	brain
30	chr6:29585400-29591800	Strong transcription	NHLF	lung
31	chr6:29585400-29592000	Strong transcription	Adipose Nuclei	Adipose
32	chr6:29585400-29592200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:29585400-29592200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:29585400-29592400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr6:29585600-29591800	Strong transcription	Primary B cells from peripheral blood	blood
36	chr6:29585600-29591800	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:29585600-29591800	Strong transcription	Fetal Lung	lung
38	chr6:29585800-29591000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr6:29585800-29591800	Strong transcription	HMEC	breast
40	chr6:29585800-29592200	Strong transcription	Fetal Muscle Leg	muscle
41	chr6:29585800-29592800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:29585800-29592800	Strong transcription	NHEK	skin
43	chr6:29586000-29592600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:29586400-29592400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr6:29586400-29592800	Weak transcription	Fetal Brain Male	brain
46	chr6:29586600-29591600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:29586600-29591800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:29586600-29591800	Strong transcription	Spleen	Spleen
49	chr6:29586800-29591200	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr6:29587000-29590800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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