Variant report

Variant	rs17178028
Chromosome Location	chr6:29593206-29593207
allele	C/G
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	USF1	chr6:29593153-29593518	H1-hESC	embryonic stem cell:	n/a	n/a
2	USF1	chr6:29593092-29593366	H1-hESC	embryonic stem cell:	n/a	n/a
3	REST	chr6:29591706-29593872	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr6:29593077-29597878	K562	blood:	n/a	n/a
5	CTBP2	chr6:29591778-29593391	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29564780..29575712-chr6:29592511..29597522,14	K562	blood:
2	chr6:28975781..28978716-chr6:29592813..29595617,2	K562	blood:

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

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12524535	0.82[AMR][1000 genomes]
rs12525400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12528017	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2267635	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28893512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28893514	0.81[EUR][1000 genomes]
rs28893515	0.81[EUR][1000 genomes]
rs28893516	0.81[EUR][1000 genomes]
rs28893517	0.81[EUR][1000 genomes]
rs28986291	0.90[AMR][1000 genomes]
rs28986295	0.81[EUR][1000 genomes]
rs28986296	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28986299	0.86[EUR][1000 genomes]
rs28986301	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28986303	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28986306	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28986307	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28986308	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29242	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3025645	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3025646	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3025649	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs362521	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3828923	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41286283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41291762	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41291766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715044	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	chr6:29574800-29595000	Weak transcription	Pancreas	Pancrea
8	chr6:29577600-29595400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:29578800-29595200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:29581800-29596000	Weak transcription	Fetal Heart	heart
11	chr6:29582600-29595400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:29589200-29595200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr6:29589200-29595400	Weak transcription	NHDF-Ad	bronchial
14	chr6:29589200-29595600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:29589400-29595000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr6:29589400-29595400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr6:29589400-29595400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:29589400-29595400	Weak transcription	HSMM	muscle
19	chr6:29589600-29594600	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:29589800-29595000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:29590200-29595200	Weak transcription	Fetal Kidney	kidney
22	chr6:29590200-29595400	Weak transcription	Esophagus	oesophagus
23	chr6:29590800-29594400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:29590800-29595200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr6:29591200-29595000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr6:29591200-29595200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr6:29591400-29594800	Weak transcription	Osteobl	bone
28	chr6:29591400-29595000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr6:29591400-29595400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr6:29591600-29593400	Weak transcription	Brain Substantia Nigra	brain
31	chr6:29591600-29594600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:29591600-29595000	Weak transcription	Left Ventricle	heart
33	chr6:29591600-29595200	Weak transcription	Lung	lung
34	chr6:29591600-29595400	Weak transcription	Aorta	Aorta
35	chr6:29591600-29595400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr6:29591600-29595600	Weak transcription	Gastric	stomach
37	chr6:29591800-29593400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr6:29591800-29593400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr6:29591800-29595000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:29591800-29595000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:29591800-29595000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:29591800-29595000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr6:29591800-29595000	Weak transcription	Ovary	ovary
44	chr6:29591800-29595000	Weak transcription	NHLF	lung
45	chr6:29591800-29595200	Weak transcription	Primary B cells from peripheral blood	blood
46	chr6:29591800-29595400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr6:29591800-29595600	Weak transcription	Spleen	Spleen
48	chr6:29591800-29595600	Weak transcription	Dnd41	blood
49	chr6:29591800-29595600	Weak transcription	HMEC	breast
50	chr6:29592000-29594000	Weak transcription	Stomach Smooth Muscle	stomach

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