Variant report

Variant	rs7579783
Chromosome Location	chr2:38762413-38762414
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38762163..38763872-chr2:38974751..38976812,2	K562	blood:
2	chr2:38760697..38762690-chr2:38978032..38979542,2	K562	blood:
3	chr2:38603492..38605404-chr2:38761964..38764089,2	K562	blood:
4	chr2:38762042..38765801-chr2:38976684..38979922,4	MCF-7	breast:
5	chr2:38760428..38762981-chr2:38976976..38979591,3	K562	blood:
6	chr2:38602731..38605404-chr2:38761964..38763937,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HNRPLL-5	chr2:38762400-38762837	NONHSAT070186

No data

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000119787	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12614876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs12616367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs12619629	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12621565	1.00[EUR][1000 genomes]
rs12621788	0.83[EUR][1000 genomes]
rs1543881	1.00[CEU][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17576044	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs17603782	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3765001	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs55785223	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55833813	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56956410	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58720388	1.00[EUR][1000 genomes]
rs59065420	1.00[EUR][1000 genomes]
rs6544165	1.00[CEU][hapmap]
rs6754893	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6760965	1.00[CEU][hapmap]
rs72895897	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72905839	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73929040	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73929052	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7578356	1.00[CHB][hapmap]
rs7584862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7606515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38755600-38762800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:38755600-38763000	Weak transcription	Esophagus	oesophagus
3	chr2:38755600-38763000	Weak transcription	Pancreas	Pancrea
4	chr2:38756000-38762800	Weak transcription	Right Atrium	heart
5	chr2:38756800-38762800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:38759600-38763000	Enhancers	Primary B cells from peripheral blood	blood
7	chr2:38759600-38763000	Weak transcription	Brain Substantia Nigra	brain
8	chr2:38759800-38763000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:38760400-38763000	Enhancers	K562	blood
10	chr2:38760600-38763200	Weak transcription	Aorta	Aorta
11	chr2:38761000-38762600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:38761000-38762600	Bivalent Enhancer	HepG2	liver
13	chr2:38761000-38763800	Active TSS	Colon Smooth Muscle	Colon
14	chr2:38761400-38763000	Enhancers	Brain Anterior Caudate	brain
15	chr2:38761600-38762600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr2:38761600-38763000	Weak transcription	Primary B cells from cord blood	blood
17	chr2:38761600-38763000	Weak transcription	GM12878-XiMat	blood
18	chr2:38762000-38763000	Bivalent Enhancer	Fetal Intestine Large	intestine
19	chr2:38762000-38763400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr2:38762200-38762600	Enhancers	Brain Cingulate Gyrus	brain
21	chr2:38762200-38762800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:38762200-38762800	Bivalent Enhancer	Placenta	Placenta
23	chr2:38762200-38762800	Active TSS	Rectal Smooth Muscle	rectum
24	chr2:38762200-38762800	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr2:38762200-38763000	Enhancers	Placenta Amnion	Placenta Amnion
26	chr2:38762200-38763400	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr2:38762200-38763800	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr2:38762200-38763800	Enhancers	Fetal Brain Male	brain
29	chr2:38762400-38762600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:38762400-38762600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
31	chr2:38762400-38762600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:38762400-38762600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:38762400-38762600	Flanking Active TSS	Colonic Mucosa	Colon
34	chr2:38762400-38762600	Weak transcription	NHEK	skin
35	chr2:38762400-38762800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
36	chr2:38762400-38762800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr2:38762400-38762800	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr2:38762400-38763000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
39	chr2:38762400-38763000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:38762400-38763000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
41	chr2:38762400-38763000	Bivalent Enhancer	Fetal Stomach	stomach
42	chr2:38762400-38763000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr2:38762400-38763200	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr2:38762400-38763600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:38762400-38763800	Active TSS	Brain Hippocampus Middle	brain

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