Variant report

Variant	rs942258
Chromosome Location	chr1:46913958-46913959
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	chr1:46912642..46915291-chr1:46916388..46919723,5	K562	blood:
2	chr1:46911310..46914050-chr1:46990566..46993135,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11211276	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11211279	0.83[EUR][1000 genomes]
rs12126376	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2281774	0.82[EUR][1000 genomes]
rs2281775	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2404584	0.83[EUR][1000 genomes]
rs4660347	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4660929	0.83[EUR][1000 genomes]
rs4660935	0.82[EUR][1000 genomes]
rs4660936	0.83[EUR][1000 genomes]
rs72637962	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7538292	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs868650	0.83[EUR][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	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS 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	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv534951	chr1:46910546-46948727	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46912400-46914600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
2	chr1:46912400-46915200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr1:46912600-46914000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
4	chr1:46912600-46914400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
5	chr1:46912600-46914600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
6	chr1:46912600-46914600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:46912800-46914000	Bivalent Enhancer	Colon Smooth Muscle	Colon
8	chr1:46912800-46914000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
9	chr1:46912800-46914000	Bivalent Enhancer	Fetal Muscle Leg	muscle
10	chr1:46912800-46914600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
11	chr1:46912800-46914600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:46913000-46914000	Bivalent Enhancer	Brain Hippocampus Middle	brain
13	chr1:46913000-46914000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr1:46913000-46914000	Bivalent Enhancer	Placenta	Placenta
15	chr1:46913200-46914400	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:46913200-46914800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr1:46913200-46915000	Weak transcription	K562	blood
18	chr1:46913400-46914000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:46913400-46914000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
20	chr1:46913400-46914000	Bivalent Enhancer	Brain Anterior Caudate	brain
21	chr1:46913400-46914000	Bivalent Enhancer	Brain Cingulate Gyrus	brain
22	chr1:46913400-46914000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
23	chr1:46913400-46914000	Bivalent Enhancer	Fetal Stomach	stomach
24	chr1:46913400-46914000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
25	chr1:46913400-46914200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:46913400-46914600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:46913400-46914600	Bivalent Enhancer	Fetal Intestine Small	intestine
28	chr1:46913400-46914600	Enhancers	Gastric	stomach
29	chr1:46913400-46914800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
30	chr1:46913600-46914000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:46913600-46914000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
32	chr1:46913600-46914000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
33	chr1:46913600-46914200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:46913600-46914200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:46913600-46914400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
36	chr1:46913600-46914400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:46913600-46914400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:46913600-46914400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:46913600-46914400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:46913600-46914400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
41	chr1:46913600-46914400	Bivalent Enhancer	Esophagus	oesophagus
42	chr1:46913600-46914600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
43	chr1:46913600-46914600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
44	chr1:46913600-46914600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:46913600-46914600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:46913600-46914600	Bivalent Enhancer	Fetal Brain Male	brain
47	chr1:46913600-46914600	Bivalent Enhancer	Lung	lung
48	chr1:46913600-46914600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
49	chr1:46913800-46914000	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:46913800-46914000	Bivalent/Poised TSS	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links