Variant report

Variant	rs6465658
Chromosome Location	chr7:97816638-97816639
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	chr7:97815298..97817791-chr7:97831369..97832934,2	MCF-7	breast:
2	chr7:97807051..97809220-chr7:97816617..97819095,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11762534	1.00[ASW][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes]
rs11763970	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11764933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11765552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11767962	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11768309	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12666406	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12670686	0.82[AMR][1000 genomes]
rs12674083	0.82[AMR][1000 genomes]
rs13221758	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17435590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17435847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2132276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34307903	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34320230	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3801294	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6465654	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6465657	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6946915	0.87[AMR][1000 genomes]
rs6951277	0.82[CEU][hapmap]
rs6958572	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6965016	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6967926	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6969384	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6977321	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7791463	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7804318	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7808528	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs940432	0.85[CEU][hapmap];0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS 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	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1816676	chr7:97676259-97868033	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv831066	chr7:97726879-97890550	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1033029	chr7:97773232-98017992	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv539033	chr7:97773232-98017992	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv888760	chr7:97816327-97965016	Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6465658	BAIAP2L1	cis	cerebellum	SCAN
rs6465658	DKFZP434B0335	cis	multi-tissue	Pritchard
rs6465658	TSC22D4	cis	cerebellum	SCAN
rs6465658	FIS1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97763400-97821000	Weak transcription	NHLF	lung
2	chr7:97765800-97840800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:97772400-97821600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr7:97782400-97819000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr7:97782400-97822000	Weak transcription	Fetal Kidney	kidney
6	chr7:97782400-97839800	Weak transcription	Fetal Brain Male	brain
7	chr7:97785200-97818600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr7:97787400-97822000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr7:97789200-97829400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr7:97793200-97822400	Weak transcription	Small Intestine	intestine
11	chr7:97793400-97818200	Weak transcription	Fetal Lung	lung
12	chr7:97793400-97841000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr7:97799400-97818400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr7:97801200-97821000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr7:97801800-97817000	Weak transcription	Colonic Mucosa	Colon
16	chr7:97802600-97816800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr7:97804400-97821000	Weak transcription	Hela-S3	cervix
18	chr7:97804400-97821200	Weak transcription	A549	lung
19	chr7:97804600-97818600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:97804600-97818600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr7:97804600-97820600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr7:97804600-97821200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr7:97804800-97818000	Weak transcription	Fetal Brain Female	brain
24	chr7:97805400-97818000	Weak transcription	Brain Germinal Matrix	brain
25	chr7:97805800-97817800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr7:97805800-97820800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr7:97807800-97816800	Weak transcription	Fetal Muscle Leg	muscle
28	chr7:97808000-97818400	Weak transcription	Aorta	Aorta
29	chr7:97808400-97833600	Weak transcription	Stomach Mucosa	stomach
30	chr7:97808600-97818200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr7:97808600-97839800	Weak transcription	Right Atrium	heart
32	chr7:97808800-97818400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr7:97808800-97818400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr7:97808800-97818400	Weak transcription	Left Ventricle	heart
35	chr7:97808800-97818400	Weak transcription	Lung	lung
36	chr7:97808800-97818600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr7:97808800-97818800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:97808800-97820800	Weak transcription	Brain Angular Gyrus	brain
39	chr7:97808800-97821000	Weak transcription	Right Ventricle	heart
40	chr7:97808800-97821600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr7:97809200-97817200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr7:97809200-97818400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr7:97809200-97818400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr7:97809200-97818400	Weak transcription	Ovary	ovary
45	chr7:97809200-97818400	Weak transcription	Thymus	Thymus
46	chr7:97809200-97818400	Weak transcription	Spleen	Spleen
47	chr7:97809200-97821000	Weak transcription	Brain Anterior Caudate	brain
48	chr7:97809200-97821000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr7:97809200-97821000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr7:97809200-97823600	Weak transcription	HMEC	breast

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