Variant report

Variant	rs8029197
Chromosome Location	chr15:59749417-59749418
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59743359..59746009-chr15:59746792..59749806,3	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10450987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10775170	0.82[EUR][1000 genomes]
rs10851658	0.88[CEU][hapmap];0.84[CHB][hapmap];0.84[EUR][1000 genomes]
rs11071447	0.80[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs11071448	0.85[CHB][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs11633115	0.84[EUR][1000 genomes]
rs11633362	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11637961	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440926	0.82[EUR][1000 genomes]
rs12913252	0.82[EUR][1000 genomes]
rs12913291	0.81[EUR][1000 genomes]
rs3803445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4078341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4334234	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4517730	0.81[EUR][1000 genomes]
rs4624109	0.86[EUR][1000 genomes]
rs4628906	0.85[EUR][1000 genomes]
rs4774331	0.92[CHB][hapmap];0.82[EUR][1000 genomes]
rs4774332	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774333	0.85[CHB][hapmap];0.82[EUR][1000 genomes]
rs4774334	0.85[CHB][hapmap];0.82[EUR][1000 genomes]
rs4774336	0.88[JPT][hapmap]
rs4775167	0.84[EUR][1000 genomes]
rs4775168	0.85[CHB][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs4775172	0.82[EUR][1000 genomes]
rs4775173	0.85[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56014137	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56041460	0.87[EUR][1000 genomes]
rs59326013	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62013060	0.87[EUR][1000 genomes]
rs62013062	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62013066	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62013067	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6494115	0.85[CHB][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs7166286	0.84[EUR][1000 genomes]
rs7172008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7175465	0.85[CHB][hapmap];0.82[EUR][1000 genomes]
rs7179571	0.84[EUR][1000 genomes]
rs7182428	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7359171	0.85[CHB][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs8024880	0.92[CHB][hapmap];0.83[EUR][1000 genomes]
rs8025789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025871	0.85[CHB][hapmap];0.82[EUR][1000 genomes]
rs8026087	0.92[CHB][hapmap];0.83[EUR][1000 genomes]
rs8026519	0.83[EUR][1000 genomes]
rs8028180	0.84[CHB][hapmap];0.85[EUR][1000 genomes]
rs8028913	0.85[CHB][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs8029746	0.92[CHB][hapmap];0.83[EUR][1000 genomes]
rs8030114	0.85[CHB][hapmap];0.81[EUR][1000 genomes]
rs8043466	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv904278	chr15:59705005-59784648	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8029197	CGNL1	cis	cerebellum	SCAN
rs8029197	CCPG1	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59730800-59754800	Weak transcription	Aorta	Aorta
2	chr15:59731400-59752200	Weak transcription	A549	lung
3	chr15:59731600-59753600	Weak transcription	Fetal Brain Female	brain
4	chr15:59731800-59753400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr15:59735400-59753800	Weak transcription	Primary B cells from cord blood	blood
6	chr15:59736400-59753400	Weak transcription	Brain Angular Gyrus	brain
7	chr15:59736800-59785000	Weak transcription	Fetal Brain Male	brain
8	chr15:59745600-59749800	Enhancers	Fetal Intestine Small	intestine
9	chr15:59747200-59753400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:59747400-59749800	Enhancers	Fetal Intestine Large	intestine
11	chr15:59748200-59749600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:59748200-59749600	Enhancers	Duodenum Mucosa	Duodenum
13	chr15:59748200-59749800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr15:59748200-59749800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:59748200-59749800	Enhancers	Placenta	Placenta
16	chr15:59748200-59749800	Enhancers	HMEC	breast
17	chr15:59748400-59752600	Weak transcription	Brain Substantia Nigra	brain
18	chr15:59748800-59749600	Enhancers	NHEK	skin
19	chr15:59749000-59755200	Weak transcription	Rectal Mucosa Donor 29	rectum

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