Variant report

Variant	rs2419117
Chromosome Location	chr1:168589182-168589183
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:168582595..168585268-chr1:168586137..168589627,3	K562	blood:
2	chr1:168587487..168589567-chr1:168600039..168601868,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10800360	0.80[ASN][1000 genomes]
rs10800364	0.89[ASN][1000 genomes]
rs10800365	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10918939	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918940	0.93[ASN][1000 genomes]
rs10918941	0.93[ASN][1000 genomes]
rs10918942	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918944	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022781	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12046540	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12047717	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12093734	0.93[ASN][1000 genomes]
rs12094908	0.93[ASN][1000 genomes]
rs1933088	0.89[ASN][1000 genomes]
rs61802611	0.83[ASN][1000 genomes]
rs6659983	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672884	0.93[EUR][1000 genomes]
rs6675068	0.80[ASN][1000 genomes]
rs6701804	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7354835	0.93[ASN][1000 genomes]
rs7354866	0.81[ASN][1000 genomes]
rs7354986	0.81[ASN][1000 genomes]
rs7355223	0.93[ASN][1000 genomes]
rs7514487	0.93[ASN][1000 genomes]
rs7522695	0.86[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7536834	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014626	chr1:168441288-168642731	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535196	chr1:168441288-168642731	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1011821	chr1:168441488-168642592	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv535197	chr1:168441488-168642592	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1008852	chr1:168449940-168643905	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv535198	chr1:168449940-168643905	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1007846	chr1:168449940-168687265	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
9	nsv831836	chr1:168538779-168716956	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv3443	chr1:168577582-168622305	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2419117	CD247	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168579000-168590200	Weak transcription	Right Atrium	heart
2	chr1:168583400-168589800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:168583800-168590800	Weak transcription	Brain Angular Gyrus	brain
4	chr1:168583800-168590800	Weak transcription	Fetal Intestine Small	intestine
5	chr1:168583800-168592200	Weak transcription	Aorta	Aorta
6	chr1:168584600-168589800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:168584600-168589800	Weak transcription	Adipose Nuclei	Adipose
8	chr1:168584600-168590600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:168584600-168592200	Weak transcription	Right Ventricle	heart
10	chr1:168584800-168589800	Weak transcription	Psoas Muscle	Psoas
11	chr1:168585200-168590600	Weak transcription	Fetal Muscle Leg	muscle
12	chr1:168585800-168589600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:168587400-168590400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:168588400-168592400	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr1:168588800-168589800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:168588800-168592600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:168588800-168592800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:168589000-168589400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links