Variant report

Variant	rs6465674
Chromosome Location	chr7:97977895-97977896
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	chr7:97943546..97945828-chr7:97977382..97980007,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10953257	0.83[ASN][1000 genomes]
rs11765794	0.83[ASN][1000 genomes]
rs12667634	0.83[ASN][1000 genomes]
rs13307593	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1468340	0.81[AFR][1000 genomes]
rs1859482	0.81[ASN][1000 genomes]
rs2240349	0.81[ASN][1000 genomes]
rs34717219	0.83[ASN][1000 genomes]
rs34835415	0.83[ASN][1000 genomes]
rs35535338	0.83[ASN][1000 genomes]
rs35997266	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs36017146	0.83[ASN][1000 genomes]
rs3801254	0.81[AFR][1000 genomes]
rs3801255	0.81[AFR][1000 genomes]
rs3801256	0.81[AFR][1000 genomes]
rs3801263	0.83[ASN][1000 genomes]
rs3823740	0.81[ASN][1000 genomes]
rs55825602	0.81[AFR][1000 genomes]
rs62478174	0.81[ASN][1000 genomes]
rs62478200	0.82[ASN][1000 genomes]
rs6465667	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6465669	0.83[ASN][1000 genomes]
rs6465670	0.83[ASN][1000 genomes]
rs6465671	0.84[ASN][1000 genomes]
rs6465672	0.83[ASN][1000 genomes]
rs6465673	0.85[ASN][1000 genomes]
rs6465675	0.83[ASN][1000 genomes]
rs6944262	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6945554	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6948346	0.83[ASN][1000 genomes]
rs6948540	0.83[ASN][1000 genomes]
rs6949214	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6959506	0.82[ASN][1000 genomes]
rs6961129	0.83[ASN][1000 genomes]
rs6961438	0.81[AFR][1000 genomes]
rs6967934	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6968321	0.83[ASN][1000 genomes]
rs6969234	0.81[AFR][1000 genomes]
rs6971825	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6974943	0.83[ASN][1000 genomes]
rs6979373	0.83[ASN][1000 genomes]
rs7777415	0.81[ASN][1000 genomes]
rs7787418	0.81[ASN][1000 genomes]
rs7787858	0.81[AFR][1000 genomes]
rs7795176	0.83[ASN][1000 genomes]
rs7801992	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7805267	0.81[ASN][1000 genomes]
rs7806739	0.81[AFR][1000 genomes]
rs7807455	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7807555	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9769767	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
9	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
10	nsv831067	chr7:97860169-98065528	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS 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	19 gene(s)	inside rSNPs	diseases
11	nsv1026477	chr7:97869446-98034129	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	nsv888766	chr7:97975542-98123880	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
13	esv3326227	chr7:97977559-97978013	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6465674	DKFZP434B0335	Cis_1M	lymphoblastoid	RTeQTL
rs6465674	BAIAP2L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97944800-97983400	Weak transcription	HepG2	liver
2	chr7:97953200-97978000	Weak transcription	Lung	lung
3	chr7:97953200-97978200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:97953800-97989800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr7:97954000-97980400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:97954400-97983800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:97958800-97981400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr7:97960200-97978400	Weak transcription	Fetal Stomach	stomach
9	chr7:97966800-97983800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr7:97968000-97982000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr7:97968200-97978200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr7:97968400-97983600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr7:97969200-97978000	Weak transcription	Gastric	stomach
14	chr7:97969200-97978000	Weak transcription	Hela-S3	cervix
15	chr7:97969200-97980600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr7:97969200-97981400	Weak transcription	Fetal Intestine Large	intestine
17	chr7:97969200-97981800	Weak transcription	Colonic Mucosa	Colon
18	chr7:97969400-97978000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:97969400-97978000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr7:97969400-97978000	Weak transcription	Esophagus	oesophagus
21	chr7:97969400-97978000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr7:97969400-97978000	Weak transcription	NHEK	skin
23	chr7:97969400-97979200	Weak transcription	HMEC	breast
24	chr7:97971200-97981600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr7:97971200-97981600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:97971200-97981600	Weak transcription	Osteobl	bone
27	chr7:97972400-97979800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr7:97972400-97983400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr7:97973000-97987000	Weak transcription	Liver	Liver
30	chr7:97973000-97989600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr7:97973200-97978000	Weak transcription	Fetal Intestine Small	intestine
32	chr7:97973200-97984000	Weak transcription	Pancreas	Pancrea
33	chr7:97973200-97989600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr7:97973400-97978200	Weak transcription	Stomach Mucosa	stomach
35	chr7:97973600-97978200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr7:97973600-97983400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr7:97975400-97978000	Weak transcription	K562	blood
38	chr7:97976600-97978000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr7:97976600-97978000	Weak transcription	A549	lung
40	chr7:97976600-97981600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr7:97977200-97979400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr7:97977200-98010200	Weak transcription	GM12878-XiMat	blood
43	chr7:97977800-97978000	Weak transcription	Duodenum Mucosa	Duodenum

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