Variant report

Variant	rs29219
Chromosome Location	chr6:29598877-29598878
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	EP300	chr6:29598637-29599444	K562	blood:	n/a	chr6:29599419-29599433 chr6:29598844-29598858
2	UBTF	chr6:29598709-29601143	K562	blood:	n/a	n/a
3	MAFF	chr6:29598857-29599273	K562	blood:	n/a	chr6:29599082-29599100
4	POLR2A	chr6:29598104-29601707	K562	blood:	n/a	n/a
5	MAZ	chr6:29598835-29601887	K562	blood:	n/a	chr6:29600301-29600311 chr6:29601521-29601531
6	ZC3H11A	chr6:29598612-29599226	K562	blood:	n/a	n/a
7	TEAD4	chr6:29598416-29599590	K562	blood:	n/a	n/a
8	CUX1	chr6:29598647-29599135	K562	blood:	n/a	n/a
9	POLR2A	chr6:29598375-29601338	K562	blood:	n/a	n/a
10	RCOR1	chr6:29598543-29601805	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:29597090..29598941-chr6:30025217..30026901,2	K562	blood:
2	chr6:29589009..29590540-chr6:29598383..29601313,2	MCF-7	breast:
3	chr6:29576532..29579299-chr6:29597327..29599166,2	K562	blood:
4	chr6:29572757..29580903-chr6:29593317..29599166,10	K562	blood:

Variant related genes	Relation type
GABBR1	TF binding region
ENSG00000204681	Chromatin interaction
ENSG00000066379	Chromatin interaction
ENSG00000204623	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]
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]
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:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29596800-29599200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
2	chr6:29596800-29600000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:29597000-29599000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:29597000-29599000	Enhancers	Primary B cells from peripheral blood	blood
5	chr6:29597000-29599200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:29597000-29599200	Weak transcription	Esophagus	oesophagus
7	chr6:29597000-29599200	Weak transcription	Gastric	stomach
8	chr6:29597000-29599200	Weak transcription	Ovary	ovary
9	chr6:29597000-29599400	Weak transcription	Aorta	Aorta
10	chr6:29597000-29599600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:29597000-29599600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:29597000-29599600	Weak transcription	Hela-S3	cervix
13	chr6:29597000-29599800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr6:29597000-29599800	Weak transcription	Pancreas	Pancrea
15	chr6:29597200-29599000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:29597200-29599000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:29597200-29599000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:29597200-29599000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:29597200-29599000	Weak transcription	Fetal Lung	lung
20	chr6:29597200-29599000	Weak transcription	Fetal Stomach	stomach
21	chr6:29597200-29599000	Enhancers	HUVEC	blood vessel
22	chr6:29597200-29599200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr6:29597200-29599200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr6:29597200-29599200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:29597200-29599200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:29597200-29599200	Weak transcription	Brain Anterior Caudate	brain
27	chr6:29597200-29599200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr6:29597200-29599200	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:29597200-29599200	Weak transcription	Left Ventricle	heart
30	chr6:29597200-29599200	Weak transcription	Lung	lung
31	chr6:29597200-29599200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr6:29597200-29599200	Weak transcription	NHLF	lung
33	chr6:29597200-29599400	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr6:29597200-29599400	Weak transcription	Brain Angular Gyrus	brain
35	chr6:29597200-29599400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:29597200-29599400	Weak transcription	Fetal Heart	heart
37	chr6:29597200-29599400	Weak transcription	Right Ventricle	heart
38	chr6:29597400-29599000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:29597400-29599600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:29597400-29599600	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr6:29597600-29599200	Weak transcription	HSMM	muscle
42	chr6:29597600-29599200	Weak transcription	NHDF-Ad	bronchial
43	chr6:29597600-29599400	Weak transcription	A549	lung
44	chr6:29597600-29599800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr6:29597600-29599800	Enhancers	Dnd41	blood
46	chr6:29597600-29599800	Weak transcription	GM12878-XiMat	blood
47	chr6:29597600-29602200	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr6:29597800-29599000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr6:29597800-29599000	Enhancers	Brain Germinal Matrix	brain
50	chr6:29597800-29599400	Weak transcription	Osteobl	bone

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