Variant report

Variant	rs6581678
Chromosome Location	chr12:66776656-66776657
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	chr12:66774714..66776959-chr12:66777282..66778823,2	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1027399	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1027400	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1027401	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1039056	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1060724	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10784525	0.95[EUR][1000 genomes]
rs1168290	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1168291	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1168292	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1168293	0.87[EUR][1000 genomes]
rs1168294	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1168295	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1168296	0.86[EUR][1000 genomes]
rs1168297	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1168298	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1168299	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1168300	0.82[CEU][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1168301	0.86[EUR][1000 genomes]
rs1168302	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1168303	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1168304	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1168305	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1168306	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1168307	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1168308	0.88[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1168309	0.84[CEU][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1168310	0.88[CEU][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs1168311	0.88[CEU][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1168314	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1168315	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1168316	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1168317	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1168318	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1168319	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1168320	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1168321	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1168322	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1168325	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1168327	0.88[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1168328	0.88[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1168329	0.88[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1168330	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1168332	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1168333	0.87[EUR][1000 genomes]
rs1168334	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1168338	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1168339	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1168340	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1168341	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1168342	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1168343	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1168344	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1168345	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1168346	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1168347	0.85[EUR][1000 genomes]
rs1168348	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1168351	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1168352	0.87[EUR][1000 genomes]
rs1168353	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1168356	0.87[EUR][1000 genomes]
rs1168357	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1168358	0.87[EUR][1000 genomes]
rs1177555	0.88[CEU][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1183272	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1183274	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1184551	0.84[EUR][1000 genomes]
rs1184552	0.87[AMR][1000 genomes]
rs1185244	0.88[CEU][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1495497	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1795529	0.82[EUR][1000 genomes]
rs2088170	0.81[EUR][1000 genomes]
rs2172881	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2951656	0.85[EUR][1000 genomes]
rs4762091	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61925898	0.88[EUR][1000 genomes]
rs6581677	0.88[CEU][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs903587	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs903589	0.87[EUR][1000 genomes]
rs903590	0.87[EUR][1000 genomes]
rs961049	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1051713	chr12:66745716-66889411	Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1040682	chr12:66750103-67328053	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6581678	SRGAP1	cis	cerebellum	SCAN
rs6581678	HELB	cis	cerebellum	SCAN
rs6581678	HELB	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66710200-66792800	Weak transcription	Fetal Kidney	kidney
2	chr12:66738000-66792800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr12:66743000-66787600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:66760200-66783200	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr12:66763600-66785200	Weak transcription	Brain Germinal Matrix	brain
6	chr12:66764200-66787200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:66764800-66780800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:66764800-66780800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr12:66765800-66780800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:66765800-66786000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:66766200-66785800	Weak transcription	Fetal Brain Female	brain
12	chr12:66769000-66780800	Weak transcription	Pancreas	Pancrea
13	chr12:66770800-66778800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:66771000-66785000	Weak transcription	Placenta	Placenta
15	chr12:66771800-66780800	Weak transcription	Primary T cells from cord blood	blood
16	chr12:66773200-66780800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:66773200-66782200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:66775200-66793000	Weak transcription	Esophagus	oesophagus
19	chr12:66775800-66780800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr12:66775800-66780800	Weak transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links