Variant report

Variant	rs12121219
Chromosome Location	chr1:120302419-120302420
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:120302129-120302444	HepG2	liver:	n/a	chr1:120302279-120302290
2	CEBPB	chr1:120302143-120302426	H1-hESC	embryonic stem cell:	n/a	chr1:120302279-120302290

No.	Distal block	Cell Line	Cell type
1	chr1:120300548..120303157-chr1:120311431..120313956,2	MCF-7	breast:
2	chr1:120300614..120303588-chr1:120307182..120308766,2	MCF-7	breast:
3	chr1:120294870..120296469-chr1:120302172..120304814,2	K562	blood:

Variant related genes	Relation type
HMGCS2	TF binding region
ENSG00000134240	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12123085	1.00[CEU][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12142268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12562383	0.83[MKK][hapmap]
rs17024167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17186233	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17258425	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4391705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4659019	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4659233	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512854	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs56239558	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv831204	chr1:120266449-120314091	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12121219	CD2	cis	parietal	SCAN
rs12121219	C1orf161	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120286800-120310000	Weak transcription	Psoas Muscle	Psoas
2	chr1:120287000-120308200	Weak transcription	Stomach Mucosa	stomach
3	chr1:120287200-120308800	Weak transcription	Fetal Kidney	kidney
4	chr1:120288000-120306800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:120289600-120306200	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr1:120290000-120303600	Strong transcription	Rectal Mucosa Donor 31	rectum
7	chr1:120290800-120302600	Strong transcription	Colonic Mucosa	Colon
8	chr1:120290800-120303600	Strong transcription	Duodenum Mucosa	Duodenum
9	chr1:120291000-120306800	Weak transcription	Esophagus	oesophagus
10	chr1:120291000-120310600	Weak transcription	Placenta	Placenta
11	chr1:120297800-120302600	Strong transcription	Fetal Intestine Large	intestine
12	chr1:120298200-120312200	Weak transcription	Right Ventricle	heart
13	chr1:120298400-120306800	Weak transcription	Gastric	stomach
14	chr1:120299400-120302600	Strong transcription	Fetal Intestine Small	intestine
15	chr1:120300200-120305200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:120301000-120306800	Weak transcription	Fetal Stomach	stomach
17	chr1:120301000-120311600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:120301600-120303200	Genic enhancers	Liver	Liver
19	chr1:120301800-120302600	Strong transcription	Left Ventricle	heart
20	chr1:120302200-120302800	Strong transcription	Rectal Smooth Muscle	rectum

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