Variant report

Variant	rs1045580
Chromosome Location	chr7:7749866-7749867
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	chr7:7749070..7751862-chr7:7752531..7755969,3	MCF-7	breast:
2	chr7:7742832..7745558-chr7:7749813..7751585,2	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10486185	1.00[CHB][hapmap]
rs11761559	1.00[CHB][hapmap]
rs11762695	1.00[CHB][hapmap]
rs11763947	1.00[CHB][hapmap]
rs11773126	0.84[AMR][1000 genomes]
rs13234396	1.00[CHB][hapmap]
rs13245945	1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[ASN][1000 genomes]
rs1468760	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1468761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17136437	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs17136498	1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[ASN][1000 genomes]
rs17169361	1.00[CHB][hapmap];0.89[CHD][hapmap]
rs17169495	1.00[CHB][hapmap]
rs17169553	1.00[CHB][hapmap]
rs17169565	1.00[CHB][hapmap]
rs17546242	1.00[CHB][hapmap]
rs1859602	1.00[CHB][hapmap]
rs1859603	1.00[CHB][hapmap]
rs1859604	1.00[CHB][hapmap]
rs2024374	0.83[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2110554	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs28912668	0.86[ASN][1000 genomes]
rs28912672	0.83[ASN][1000 genomes]
rs28914835	0.97[ASN][1000 genomes]
rs28915973	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs28916271	1.00[CHB][hapmap];0.89[CHD][hapmap]
rs28992773	1.00[CHB][hapmap];0.89[CHD][hapmap]
rs35209697	0.86[ASN][1000 genomes]
rs3757526	1.00[CHB][hapmap]
rs4720745	1.00[CHB][hapmap]
rs4720746	1.00[CHB][hapmap]
rs4720747	1.00[CHB][hapmap]
rs6950845	1.00[CHB][hapmap];0.81[MEX][hapmap]
rs6955624	1.00[CHB][hapmap]
rs6964727	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6972655	1.00[CHB][hapmap]
rs7791543	1.00[CHB][hapmap]
rs7794467	1.00[CHB][hapmap]
rs7800009	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7810800	1.00[CHB][hapmap]
rs9692373	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
3	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	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
5	nsv8043	chr7:7589195-7862802	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	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
7	nsv887479	chr7:7681131-7779091	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	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
9	nsv887481	chr7:7681576-7779324	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv887482	chr7:7682439-7785047	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv887483	chr7:7682439-7798217	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv887484	chr7:7692483-7769363	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	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
14	nsv606045	chr7:7704889-7755491	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv887486	chr7:7712498-7785047	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	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
17	nsv1026564	chr7:7734846-7897847	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
18	nsv887487	chr7:7740914-7802561	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1045580	CYTH3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7722000-7750600	Weak transcription	Primary B cells from cord blood	blood
2	chr7:7737600-7778800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr7:7740000-7759000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:7743600-7762800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:7743600-7772800	Weak transcription	Gastric	stomach
6	chr7:7745600-7758800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:7745800-7750000	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr7:7746000-7762400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr7:7746600-7751800	Weak transcription	Dnd41	blood
10	chr7:7746800-7750000	Enhancers	H1 Cell Line	embryonic stem cell
11	chr7:7747200-7753200	Weak transcription	GM12878-XiMat	blood
12	chr7:7747800-7763800	Weak transcription	Left Ventricle	heart
13	chr7:7748000-7750000	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr7:7748200-7772200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr7:7749000-7750000	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr7:7749200-7753400	Weak transcription	Fetal Thymus	thymus
17	chr7:7749200-7757200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr7:7749200-7758800	Weak transcription	Primary T cells from cord blood	blood
19	chr7:7749200-7770800	Weak transcription	Small Intestine	intestine
20	chr7:7749400-7754200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr7:7749400-7756000	Weak transcription	Fetal Intestine Small	intestine
22	chr7:7749600-7750000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr7:7749600-7753400	Weak transcription	Brain Germinal Matrix	brain
24	chr7:7749800-7754000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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