Variant report

Variant	rs3025640
Chromosome Location	chr6:29570665-29570666
allele	A/G
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	chr6:29566358..29568865-chr6:29570413..29572313,3	K562	blood:
4	chr6:29566782..29572750-chr6:29592808..29598864,8	K562	blood:

Variant related genes	Relation type
ENSG00000204681	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17184388	0.89[ASN][1000 genomes]
rs17218739	0.89[ASN][1000 genomes]
rs2076482	0.81[ASN][1000 genomes]
rs2267634	0.89[ASN][1000 genomes]
rs28359962	0.81[EUR][1000 genomes]
rs28359968	0.81[EUR][1000 genomes]
rs28359990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28359991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55650674	0.89[ASN][1000 genomes]
rs55662018	0.89[ASN][1000 genomes]
rs56381026	0.89[ASN][1000 genomes]
rs61744969	0.89[ASN][1000 genomes]
rs61997184	0.89[ASN][1000 genomes]
rs740884	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9258000	0.81[ASN][1000 genomes]
rs9258033	0.81[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3025640	HLA-L	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29561600-29571600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:29561800-29571600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:29561800-29573200	Weak transcription	HSMMtube	muscle
4	chr6:29562000-29571800	Weak transcription	Left Ventricle	heart
5	chr6:29562000-29572600	Weak transcription	Fetal Heart	heart
6	chr6:29565600-29572200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr6:29566400-29595200	Weak transcription	Right Atrium	heart
8	chr6:29566600-29587000	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr6:29566800-29570800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:29566800-29570800	Weak transcription	Colon Smooth Muscle	Colon
11	chr6:29566800-29571400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr6:29566800-29571800	Strong transcription	Fetal Brain Female	brain
13	chr6:29566800-29572000	Weak transcription	Pancreas	Pancrea
14	chr6:29566800-29572400	Weak transcription	HUVEC	blood vessel
15	chr6:29566800-29584600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:29566800-29590000	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr6:29566800-29590600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:29567000-29571000	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:29567000-29571200	Weak transcription	Brain Angular Gyrus	brain
20	chr6:29567000-29571800	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr6:29567000-29589800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:29567200-29571800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:29567200-29571800	Weak transcription	Esophagus	oesophagus
24	chr6:29567200-29589400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr6:29567200-29589800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:29567400-29572000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
27	chr6:29567600-29574600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:29567600-29583800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:29567600-29592400	Strong transcription	Fetal Stomach	stomach
30	chr6:29567600-29595400	Weak transcription	A549	lung
31	chr6:29567800-29571600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:29567800-29572000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr6:29567800-29582800	Strong transcription	Ovary	ovary
34	chr6:29567800-29584600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:29568000-29571600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr6:29568000-29572200	Weak transcription	Primary T cells from cord blood	blood
37	chr6:29568000-29574600	Weak transcription	HSMM	muscle
38	chr6:29568200-29572000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr6:29568200-29572800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:29568400-29572400	Weak transcription	Dnd41	blood
41	chr6:29568400-29582600	Strong transcription	HMEC	breast
42	chr6:29568400-29583600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr6:29568600-29570800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr6:29568600-29595200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr6:29568800-29572200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr6:29568800-29578000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr6:29568800-29583200	Strong transcription	NHEK	skin
48	chr6:29569000-29570800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
49	chr6:29569000-29582600	Strong transcription	Primary B cells from peripheral blood	blood
50	chr6:29569000-29582800	Strong transcription	Osteobl	bone

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