Variant report

Variant	rs12562746
Chromosome Location	chr1:241758894-241758895
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:241758385..241760120-chr1:241802525..241804678,2	K562	blood:
2	chr1:241730497..241733176-chr1:241756519..241759419,2	K562	blood:

Variant related genes	Relation type
ENSG00000054277	Chromatin interaction
ENSG00000117009	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11586782	1.00[AFR][1000 genomes]
rs11587755	1.00[AFR][1000 genomes]
rs11590381	1.00[AFR][1000 genomes]
rs12568853	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16841866	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273712	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41269375	1.00[AFR][1000 genomes]
rs45614438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56176170	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
9	nsv427963	chr1:241718799-241832833	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241740200-241759600	Strong transcription	Primary B cells from peripheral blood	blood
2	chr1:241740400-241768800	Weak transcription	Spleen	Spleen
3	chr1:241743200-241768600	Weak transcription	Esophagus	oesophagus
4	chr1:241746600-241779200	Weak transcription	Lung	lung
5	chr1:241746800-241761400	Weak transcription	GM12878-XiMat	blood
6	chr1:241746800-241779600	Weak transcription	Aorta	Aorta
7	chr1:241749200-241760000	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:241749400-241760200	Strong transcription	Liver	Liver
9	chr1:241750000-241759600	Strong transcription	Primary B cells from cord blood	blood
10	chr1:241750600-241771600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:241750600-241786000	Weak transcription	Fetal Brain Female	brain
12	chr1:241750800-241759200	Weak transcription	Fetal Brain Male	brain
13	chr1:241750800-241768800	Weak transcription	Fetal Kidney	kidney
14	chr1:241750800-241771800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:241750800-241773400	Weak transcription	Brain Angular Gyrus	brain
16	chr1:241750800-241774600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:241750800-241786200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:241752600-241773400	Weak transcription	Gastric	stomach
19	chr1:241753400-241761000	Weak transcription	HepG2	liver
20	chr1:241753400-241791200	Weak transcription	Thymus	Thymus
21	chr1:241753800-241759600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:241754200-241759400	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:241754200-241759600	Weak transcription	K562	blood
24	chr1:241754200-241773600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:241754400-241760000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:241754400-241782600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:241754800-241760000	Weak transcription	Fetal Intestine Small	intestine
28	chr1:241755000-241760200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:241755000-241760200	Weak transcription	HSMMtube	muscle
30	chr1:241755000-241777600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:241755400-241764000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:241755600-241767000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:241755600-241773000	Weak transcription	Brain Germinal Matrix	brain
34	chr1:241755800-241767000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:241755800-241775800	Weak transcription	Adipose Nuclei	Adipose
36	chr1:241756000-241761600	Weak transcription	HSMM	muscle
37	chr1:241756000-241766800	Weak transcription	NH-A	brain
38	chr1:241756000-241769200	Weak transcription	Psoas Muscle	Psoas
39	chr1:241756000-241771000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:241756000-241791000	Weak transcription	Fetal Thymus	thymus
41	chr1:241756200-241759000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:241756200-241763400	Weak transcription	Dnd41	blood
43	chr1:241756200-241767600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:241756400-241760600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr1:241756400-241762000	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr1:241756400-241773400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:241756400-241774600	Weak transcription	Small Intestine	intestine
48	chr1:241756400-241779000	Weak transcription	Colonic Mucosa	Colon
49	chr1:241756600-241766400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:241756800-241771600	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links