Variant report

Variant	rs17186233
Chromosome Location	chr1:120297163-120297164
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	chr1:120295229..120298701-chr1:120300751..120303479,3	MCF-7	breast:

Variant related genes	Relation type
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]
rs12121219	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]
rs12123085	1.00[CEU][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12142268	1.00[CHB][hapmap];1.00[JPT][hapmap]
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];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17258425	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4391705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4659019	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[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];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs512854	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs56239558	0.86[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
rs17186233	C1orf161	cis	parietal	SCAN
rs17186233	CD2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120286800-120297800	Weak transcription	Right Ventricle	heart
2	chr1:120286800-120302200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:120286800-120310000	Weak transcription	Psoas Muscle	Psoas
4	chr1:120287000-120301800	Weak transcription	Left Ventricle	heart
5	chr1:120287000-120308200	Weak transcription	Stomach Mucosa	stomach
6	chr1:120287200-120308800	Weak transcription	Fetal Kidney	kidney
7	chr1:120288000-120306800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:120289600-120306200	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr1:120290000-120303600	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr1:120290800-120301600	Strong transcription	Liver	Liver
11	chr1:120290800-120302600	Strong transcription	Colonic Mucosa	Colon
12	chr1:120290800-120303600	Strong transcription	Duodenum Mucosa	Duodenum
13	chr1:120291000-120306800	Weak transcription	Esophagus	oesophagus
14	chr1:120291000-120310600	Weak transcription	Placenta	Placenta
15	chr1:120291600-120299400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:120292200-120299600	Weak transcription	Fetal Stomach	stomach
17	chr1:120292400-120297800	Weak transcription	Gastric	stomach
18	chr1:120295200-120297800	Weak transcription	Fetal Intestine Large	intestine
19	chr1:120296400-120298600	Strong transcription	Fetal Intestine Small	intestine
20	chr1:120296600-120298600	Strong transcription	Sigmoid Colon	Sigmoid Colon

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