Variant report

Variant	rs7971288
Chromosome Location	chr12:25297907-25297908
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:25297460..25298286-chr6:10162370..10163071,2	MCF-7	breast:
2	chr12:25293184..25295651-chr12:25296801..25299581,2	K562	blood:

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10505959	1.00[CHB][hapmap]
rs10505960	0.82[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10771166	1.00[CHB][hapmap]
rs10771169	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10771171	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771174	0.89[CHB][hapmap]
rs10771175	1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs10771176	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs10842464	1.00[CHB][hapmap]
rs10842469	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10842470	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10842471	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10842472	0.90[ASN][1000 genomes]
rs10842473	0.82[AFR][1000 genomes]
rs10842475	0.93[AFR][1000 genomes]
rs10842476	0.92[ASN][1000 genomes]
rs10842478	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10842483	0.92[ASN][1000 genomes]
rs10842488	0.82[ASN][1000 genomes]
rs10842490	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10842491	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10842492	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs10842495	0.82[ASN][1000 genomes]
rs10842498	1.00[YRI][hapmap]
rs10842515	0.89[JPT][hapmap]
rs10842516	0.89[JPT][hapmap]
rs10842517	0.89[JPT][hapmap]
rs11047825	0.88[CHB][hapmap]
rs11047852	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11047854	0.93[AFR][1000 genomes]
rs11047855	0.93[AFR][1000 genomes]
rs11047856	0.93[AFR][1000 genomes]
rs11047858	0.89[CHB][hapmap];0.90[ASN][1000 genomes]
rs11047862	0.92[ASN][1000 genomes]
rs11047865	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs11047885	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs11047912	0.89[JPT][hapmap]
rs11047914	0.89[JPT][hapmap]
rs11047917	0.89[JPT][hapmap]
rs11513449	0.86[AFR][1000 genomes]
rs11834088	1.00[CHB][hapmap]
rs12227966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12228638	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12367971	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs12424685	0.93[AFR][1000 genomes]
rs12818169	0.93[AFR][1000 genomes]
rs12828609	0.93[AFR][1000 genomes]
rs12830058	0.93[AFR][1000 genomes]
rs12830336	0.83[AFR][1000 genomes]
rs1497253	0.89[CHB][hapmap]
rs17329025	0.82[MKK][hapmap];1.00[YRI][hapmap]
rs17388587	0.89[JPT][hapmap]
rs17389103	0.89[JPT][hapmap]
rs2220196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2291365	0.84[ASW][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2352782	0.83[ASW][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs2352784	0.86[AFR][1000 genomes]
rs2883030	0.90[ASN][1000 genomes]
rs3924650	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs4313666	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs4368021	0.89[JPT][hapmap]
rs4559767	0.86[AFR][1000 genomes]
rs4589388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4963850	0.83[AFR][1000 genomes]
rs55950027	0.82[ASN][1000 genomes]
rs61020746	0.88[AFR][1000 genomes]
rs6487456	0.83[AFR][1000 genomes]
rs6487458	0.90[ASN][1000 genomes]
rs7133640	0.89[JPT][hapmap]
rs7133904	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7134616	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7135130	0.90[ASN][1000 genomes]
rs7303373	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs7303669	1.00[CHB][hapmap]
rs7309670	0.88[JPT][hapmap]
rs7315339	0.89[JPT][hapmap]
rs7956818	0.90[ASN][1000 genomes]
rs7960428	1.00[CHB][hapmap]
rs7960917	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7971062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973365	0.90[ASN][1000 genomes]
rs7973450	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7975271	1.00[CHB][hapmap]
rs7976254	1.00[CHB][hapmap]
rs7976355	0.82[JPT][hapmap]
rs7980769	1.00[CHB][hapmap];0.89[JPT][hapmap]

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	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh 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	30 gene(s)	inside rSNPs	diseases
4	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1041218	chr12:24972019-25304356	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv557796	chr12:25266203-25306458	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv515612	chr12:25272027-25341177	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv557797	chr12:25272027-25341177	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv898922	chr12:25274593-25408047	Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7971288	GOLT1B	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25286800-25304200	Weak transcription	Ovary	ovary
2	chr12:25293800-25303000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:25297400-25298400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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