Variant report

Variant	rs6972069
Chromosome Location	chr7:7531268-7531269
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:7528603..7532505-chr7:7533349..7536188,3	K562	blood:
2	chr7:7531005..7532947-chr7:7534688..7536787,2	K562	blood:
3	chr7:7530006..7532448-chr7:7539748..7541894,2	MCF-7	breast:
4	chr7:7521873..7525191-chr7:7530979..7533379,3	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10225403	0.90[JPT][hapmap]
rs10234554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10235363	0.84[CEU][hapmap]
rs10235505	0.84[CEU][hapmap]
rs10236946	0.90[JPT][hapmap]
rs10244711	0.86[JPT][hapmap]
rs10246954	0.90[JPT][hapmap]
rs1024715	0.84[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs10263223	0.90[JPT][hapmap]
rs10280546	0.82[JPT][hapmap]
rs11772657	1.00[JPT][hapmap]
rs11982762	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12671912	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1294598	0.90[JPT][hapmap]
rs1297791	0.84[CEU][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap]
rs17167804	0.90[JPT][hapmap]
rs17167922	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17168217	1.00[JPT][hapmap]
rs17168290	1.00[JPT][hapmap]
rs1860724	0.83[CEU][hapmap]
rs2348046	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs28522448	0.86[ASN][1000 genomes]
rs4455736	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55745506	0.96[ASN][1000 genomes]
rs55954412	0.96[ASN][1000 genomes]
rs56058922	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56913410	0.96[ASN][1000 genomes]
rs58115252	0.96[ASN][1000 genomes]
rs61404535	0.96[ASN][1000 genomes]
rs6463692	0.82[JPT][hapmap]
rs6463694	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6463695	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6946064	1.00[JPT][hapmap]
rs6946659	0.84[CEU][hapmap]
rs6946913	1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MKK][hapmap]
rs6947175	1.00[JPT][hapmap]
rs6948300	0.90[JPT][hapmap]
rs6950825	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6952195	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6954909	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6957099	0.90[JPT][hapmap]
rs6957880	1.00[JPT][hapmap]
rs6967835	0.90[JPT][hapmap]
rs725934	0.90[JPT][hapmap]
rs7459128	0.90[JPT][hapmap]
rs7789262	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7800860	1.00[JPT][hapmap]
rs929378	0.90[JPT][hapmap]
rs929379	1.00[JPT][hapmap]
rs972766	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869091	chr7:6927461-7567820	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv1030246	chr7:7053923-7569633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers 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 target site	84 gene(s)	inside rSNPs	diseases
7	nsv887470	chr7:7310023-7655094	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv887472	chr7:7405069-7680697	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
10	nsv606043	chr7:7473563-7571420	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv887473	chr7:7497676-7604913	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1027872	chr7:7516124-7600842	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1024107	chr7:7516124-7601638	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv887474	chr7:7519603-7679644	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
15	nsv887475	chr7:7519603-7679644	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
16	nsv887476	chr7:7519603-7680697	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6972069	COL28A1	cis	cerebellum	SCAN
rs6972069	C7orf70	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7528000-7531400	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr7:7528000-7545600	Weak transcription	Placenta	Placenta
3	chr7:7528600-7575400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr7:7528800-7532200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr7:7529000-7532000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr7:7529000-7532200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr7:7529000-7532200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:7529000-7557600	Weak transcription	Pancreas	Pancrea
9	chr7:7529200-7531400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:7529200-7531400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr7:7529200-7531800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr7:7529200-7532200	Enhancers	HSMM	muscle
13	chr7:7529200-7533600	Enhancers	Hela-S3	cervix
14	chr7:7529400-7531800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr7:7529400-7532200	Enhancers	NHDF-Ad	bronchial
16	chr7:7529400-7533800	Enhancers	Osteobl	bone
17	chr7:7529800-7533800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr7:7530400-7532800	Weak transcription	HMEC	breast
19	chr7:7530600-7531800	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr7:7530800-7532200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr7:7531000-7531600	Enhancers	NHLF	lung
22	chr7:7531200-7531800	Enhancers	HepG2	liver
23	chr7:7531200-7532200	Enhancers	Fetal Intestine Small	intestine
24	chr7:7531200-7532200	Enhancers	A549	lung

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