Variant report

Variant	rs6973081
Chromosome Location	chr7:102526866-102526867
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	chr7:102526206..102528003-chr7:102535680..102538379,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10267275	0.81[YRI][hapmap]
rs10487279	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10499952	0.82[ASW][hapmap];0.81[LWK][hapmap];0.92[MKK][hapmap];0.81[AFR][1000 genomes]
rs1057066	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11972019	0.89[YRI][hapmap]
rs11972644	0.89[YRI][hapmap]
rs11978670	0.90[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.90[YRI][hapmap]
rs11978768	0.89[YRI][hapmap]
rs11982617	0.96[EUR][1000 genomes]
rs11983456	0.89[YRI][hapmap]
rs11983521	0.88[MEX][hapmap];0.90[YRI][hapmap]
rs12056296	0.85[AFR][1000 genomes]
rs12530741	0.85[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap]
rs12537821	0.95[CHD][hapmap];0.89[JPT][hapmap]
rs12666764	0.86[YRI][hapmap]
rs12669668	0.88[MEX][hapmap];0.81[MKK][hapmap]
rs2009503	0.89[YRI][hapmap];0.89[AFR][1000 genomes]
rs4357217	0.89[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.89[ASN][1000 genomes]
rs4400322	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57368671	0.85[AFR][1000 genomes]
rs61404409	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61679881	0.84[AFR][1000 genomes]
rs6465877	0.82[ASW][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.90[YRI][hapmap]
rs6465879	0.90[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.90[YRI][hapmap]
rs6465885	0.90[ASW][hapmap];0.84[LWK][hapmap];0.90[MKK][hapmap];0.81[AFR][1000 genomes]
rs6942855	0.90[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.90[YRI][hapmap]
rs6945369	0.80[YRI][hapmap]
rs6946773	0.81[LWK][hapmap];0.86[MKK][hapmap];0.85[YRI][hapmap]
rs6952186	0.92[ASN][1000 genomes]
rs6956781	0.90[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs6957434	0.90[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs6957771	0.83[AFR][1000 genomes]
rs6967389	0.81[LWK][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.90[YRI][hapmap]
rs6975451	0.90[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.90[YRI][hapmap]
rs73406302	0.84[AFR][1000 genomes]
rs73408204	0.84[AFR][1000 genomes]
rs73408241	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73408250	0.81[AFR][1000 genomes]
rs73408272	0.88[EUR][1000 genomes]
rs7779121	0.89[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.84[YRI][hapmap];0.81[ASN][1000 genomes]
rs7779618	0.89[YRI][hapmap];0.83[AFR][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	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv470382	chr7:102375663-102538515	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv608057	chr7:102440184-102538515	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv608058	chr7:102466741-102571713	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv464667	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	nsv608060	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
10	nsv5880	chr7:102505158-102550471	Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6973081	LRWD1	cis	cerebellum	SCAN
rs6973081	SH2B2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102501200-102530800	Weak transcription	Ovary	ovary
2	chr7:102508000-102529200	Weak transcription	Fetal Lung	lung
3	chr7:102513800-102531600	Weak transcription	Fetal Brain Male	brain
4	chr7:102515600-102527400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr7:102517000-102549600	Weak transcription	Gastric	stomach
6	chr7:102517200-102529600	Weak transcription	NHLF	lung
7	chr7:102517200-102578200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr7:102522000-102527000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr7:102522600-102529600	Weak transcription	Fetal Stomach	stomach
10	chr7:102522600-102549200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:102524200-102529000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr7:102524200-102529000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr7:102524200-102529600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr7:102524800-102528200	Weak transcription	A549	lung
15	chr7:102524800-102528600	Weak transcription	HUVEC	blood vessel
16	chr7:102524800-102528800	Weak transcription	Stomach Mucosa	stomach
17	chr7:102525400-102527600	Weak transcription	K562	blood
18	chr7:102526000-102530800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr7:102526200-102528600	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr7:102526600-102528200	Enhancers	Primary monocytes fromperipheralblood	blood

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