Variant report

Variant	rs17562004
Chromosome Location	chr7:7902369-7902370
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:7900050..7902879-chr7:7904701..7906476,3	K562	blood:
2	chr7:7896335..7897890-chr7:7900322..7902717,2	MCF-7	breast:
3	chr7:7866665..7868204-chr7:7899754..7902407,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10260454	1.00[ASW][hapmap];0.83[CEU][hapmap];0.86[MEX][hapmap]
rs10952076	0.93[ASN][1000 genomes]
rs11761203	1.00[YRI][hapmap]
rs11770981	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12534077	0.90[ASN][1000 genomes]
rs17496091	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17496427	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17561662	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2348763	0.96[CEU][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4270868	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6463729	0.95[ASN][1000 genomes]
rs6951789	0.90[ASN][1000 genomes]
rs6959805	0.81[AMR][1000 genomes]
rs6965111	0.93[ASN][1000 genomes]
rs6966260	0.92[ASN][1000 genomes]
rs73061204	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73061208	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73061237	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73061244	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7784704	0.91[ASN][1000 genomes]
rs7790025	0.95[ASN][1000 genomes]
rs7808919	0.95[ASN][1000 genomes]

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	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
2	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv887478	chr7:7670718-7917360	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv887480	chr7:7681131-7917360	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv887485	chr7:7692483-7917360	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv887489	chr7:7770203-7913311	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1027770	chr7:7797431-7957507	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv538722	chr7:7797431-7957507	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv887490	chr7:7801684-7908970	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv523479	chr7:7821594-7909899	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv917172	chr7:7854632-8807385	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
13	nsv1030180	chr7:7860424-8059221	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
14	nsv1027123	chr7:7870047-7926288	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	esv1793003	chr7:7902171-7911371	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	esv3449658	chr7:7902183-7902433	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17562004	CDH22	trans	parietal	SCAN
rs17562004	ZNF12	cis	parietal	SCAN
rs17562004	MMD2	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7892200-7906800	Weak transcription	Fetal Heart	heart
2	chr7:7895400-7906400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:7895400-7907000	Weak transcription	Thymus	Thymus
4	chr7:7895400-7908800	Weak transcription	Left Ventricle	heart
5	chr7:7895400-7918000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr7:7895800-7902600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr7:7896000-7907600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:7897200-7909000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:7897200-7923200	Weak transcription	Psoas Muscle	Psoas
10	chr7:7897200-7942400	Weak transcription	Aorta	Aorta
11	chr7:7898400-7907200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr7:7899000-7907000	Weak transcription	Primary B cells from cord blood	blood
13	chr7:7900400-7902400	Enhancers	Hela-S3	cervix
14	chr7:7900400-7904200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr7:7900600-7902400	Enhancers	HMEC	breast
16	chr7:7900600-7903200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr7:7901200-7915600	Weak transcription	Gastric	stomach
18	chr7:7901400-7903600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr7:7902200-7902400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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