Variant report

Variant	rs3025642
Chromosome Location	chr6:29570316-29570317
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:29567658..29569553-chr6:29570192..29572225,2	K562	blood:
2	chr6:29564780..29575712-chr6:29592511..29597522,14	K562	blood:
3	chr6:29566782..29572750-chr6:29592808..29598864,8	K562	blood:

Variant related genes	Relation type
ENSG00000204681	Chromatin interaction

Extended variants
information (count: 41 )
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]
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:5 , 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
3	nsv528285	chr6:29566842-29588146	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv462671	chr6:29566842-29588146	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv601229	chr6:29566842-29588146	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29561600-29570600	Weak transcription	Right Ventricle	heart
2	chr6:29561600-29571600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:29561800-29571600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:29561800-29573200	Weak transcription	HSMMtube	muscle
5	chr6:29562000-29570600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:29562000-29571800	Weak transcription	Left Ventricle	heart
7	chr6:29562000-29572600	Weak transcription	Fetal Heart	heart
8	chr6:29565600-29570400	Weak transcription	NHDF-Ad	bronchial
9	chr6:29565600-29572200	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr6:29566400-29595200	Weak transcription	Right Atrium	heart
11	chr6:29566600-29570400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:29566600-29587000	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr6:29566800-29570400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr6:29566800-29570600	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr6:29566800-29570800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:29566800-29570800	Weak transcription	Colon Smooth Muscle	Colon
17	chr6:29566800-29571400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:29566800-29571800	Strong transcription	Fetal Brain Female	brain
19	chr6:29566800-29572000	Weak transcription	Pancreas	Pancrea
20	chr6:29566800-29572400	Weak transcription	HUVEC	blood vessel
21	chr6:29566800-29584600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:29566800-29590000	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr6:29566800-29590600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:29567000-29570400	Weak transcription	Primary B cells from cord blood	blood
25	chr6:29567000-29570400	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr6:29567000-29571000	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr6:29567000-29571200	Weak transcription	Brain Angular Gyrus	brain
28	chr6:29567000-29571800	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr6:29567000-29589800	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:29567200-29571800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:29567200-29571800	Weak transcription	Esophagus	oesophagus
32	chr6:29567200-29589400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr6:29567200-29589800	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:29567400-29570600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:29567400-29572000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
36	chr6:29567600-29570400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:29567600-29570600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:29567600-29574600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:29567600-29583800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:29567600-29592400	Strong transcription	Fetal Stomach	stomach
41	chr6:29567600-29595400	Weak transcription	A549	lung
42	chr6:29567800-29571600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:29567800-29572000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr6:29567800-29582800	Strong transcription	Ovary	ovary
45	chr6:29567800-29584600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:29568000-29571600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:29568000-29572200	Weak transcription	Primary T cells from cord blood	blood
48	chr6:29568000-29574600	Weak transcription	HSMM	muscle
49	chr6:29568200-29572000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr6:29568200-29572800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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