Variant report

Variant	rs2798246
Chromosome Location	chr1:112983349-112983350
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:112967128..112969629-chr1:112981211..112983831,2	K562	blood:
2	chr1:112973405..112975410-chr1:112980572..112983534,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1175624	0.84[AFR][1000 genomes]
rs1175627	1.00[YRI][hapmap]
rs1175628	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1175637	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1175639	1.00[YRI][hapmap]
rs1175640	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1175642	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1175643	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1777621	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2483347	0.88[AFR][1000 genomes]
rs2780274	1.00[AMR][1000 genomes]
rs2780276	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][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	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers 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 miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1850997	chr1:112944472-112993754	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:112942400-112988200	Weak transcription	Small Intestine	intestine
2	chr1:112952400-112990600	Weak transcription	Esophagus	oesophagus
3	chr1:112957400-112986600	Weak transcription	NHLF	lung
4	chr1:112957600-112997600	Weak transcription	Brain Anterior Caudate	brain
5	chr1:112959600-112991600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:112959800-112992800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:112960000-112995200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:112960000-112996800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:112960200-112991600	Weak transcription	Hela-S3	cervix
10	chr1:112960400-112991400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:112961200-112995600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:112961800-112986800	Weak transcription	HMEC	breast
13	chr1:112962000-112990800	Weak transcription	Fetal Brain Male	brain
14	chr1:112962600-112990400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:112962600-112991600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:112965800-112986400	Weak transcription	NHDF-Ad	bronchial
17	chr1:112965800-112996200	Weak transcription	Placenta	Placenta
18	chr1:112967000-112991600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:112968600-112986600	Weak transcription	NHEK	skin
20	chr1:112968600-112987400	Weak transcription	Fetal Intestine Large	intestine
21	chr1:112968600-112987600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:112968600-112990600	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:112968600-112994800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:112968600-112995400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:112968600-112995600	Weak transcription	Colonic Mucosa	Colon
26	chr1:112972200-112991400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:112973400-112985400	Weak transcription	Left Ventricle	heart
28	chr1:112973600-112988800	Weak transcription	Lung	lung
29	chr1:112974000-112997000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:112975600-112984200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:112976200-112994200	Weak transcription	Psoas Muscle	Psoas
32	chr1:112977600-112986600	Weak transcription	NH-A	brain
33	chr1:112979400-112988800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:112979600-112990000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:112979600-112990800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:112979600-112998600	Weak transcription	Right Ventricle	heart
37	chr1:112979600-112998600	Weak transcription	Spleen	Spleen
38	chr1:112979800-112983800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:112979800-112983800	Weak transcription	Fetal Kidney	kidney
40	chr1:112979800-112986000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:112979800-112986000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:112979800-112986200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:112979800-112986400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:112979800-112987400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:112979800-112987600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:112979800-112990800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr1:112979800-112992000	Weak transcription	Brain Angular Gyrus	brain
48	chr1:112979800-112992200	Weak transcription	Brain Germinal Matrix	brain
49	chr1:112980000-112988200	Weak transcription	GM12878-XiMat	blood
50	chr1:112981000-112997200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links