Variant report

Variant	rs12409248
Chromosome Location	chr1:120338418-120338419
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120336862..120340464-chr1:120344663..120347846,4	MCF-7	breast:
2	chr1:120315709..120317268-chr1:120336953..120338874,2	MCF-7	breast:
3	chr1:120329924..120336261-chr1:120336777..120341772,6	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10754419	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10923899	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10923901	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12070819	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12071960	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12073231	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12076466	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12080486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12086303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12094770	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12408507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12408976	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28522608	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3213910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs729233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73000454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer 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 miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv915933	chr1:120323527-120471049	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv831226	chr1:120331599-120471049	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120332800-120341600	Enhancers	Fetal Stomach	stomach
2	chr1:120333800-120339200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:120334000-120339400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:120335800-120338800	Enhancers	Duodenum Smooth Muscle	Duodenum
5	chr1:120336000-120338600	Enhancers	Fetal Muscle Leg	muscle
6	chr1:120336000-120338800	Enhancers	Fetal Intestine Large	intestine
7	chr1:120336000-120338800	Enhancers	Stomach Mucosa	stomach
8	chr1:120336000-120340200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:120336000-120341600	Weak transcription	Primary T cells from cord blood	blood
10	chr1:120336000-120349400	Weak transcription	Right Atrium	heart
11	chr1:120336200-120338800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:120336200-120339600	Enhancers	Colon Smooth Muscle	Colon
13	chr1:120336400-120342200	Weak transcription	Spleen	Spleen
14	chr1:120337000-120338600	Enhancers	Colonic Mucosa	Colon
15	chr1:120337000-120338800	Enhancers	Duodenum Mucosa	Duodenum
16	chr1:120337000-120340000	Enhancers	Fetal Lung	lung
17	chr1:120337200-120339600	Enhancers	Rectal Smooth Muscle	rectum
18	chr1:120337200-120340000	Enhancers	Fetal Intestine Small	intestine
19	chr1:120337800-120338800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:120337800-120338800	Genic enhancers	Pancreas	Pancrea
21	chr1:120337800-120338800	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr1:120337800-120338800	Enhancers	HMEC	breast
23	chr1:120337800-120339600	Enhancers	Placenta	Placenta
24	chr1:120338000-120338600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr1:120338000-120338600	Weak transcription	Fetal Kidney	kidney
26	chr1:120338000-120338600	Enhancers	Small Intestine	intestine
27	chr1:120338000-120338800	Enhancers	Esophagus	oesophagus
28	chr1:120338000-120338800	Bivalent Enhancer	HepG2	liver
29	chr1:120338000-120340200	Enhancers	Stomach Smooth Muscle	stomach
30	chr1:120338200-120338600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:120338200-120338600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:120338400-120338600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links