Variant report

Variant	rs4729617
Chromosome Location	chr7:100473729-100473730
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100392056..100394261-chr7:100473192..100475486,2	MCF-7	breast:
2	chr7:100448186..100450905-chr7:100471509..100474207,3	K562	blood:
3	chr7:100470889..100475047-chr7:100805272..100809585,4	MCF-7	breast:
4	chr7:100410860..100413400-chr7:100471850..100474655,4	MCF-7	breast:
5	chr2:232573730..232575283-chr7:100471498..100474384,2	MCF-7	breast:
6	chr7:100301991..100304914-chr7:100472265..100475755,3	MCF-7	breast:
7	chr7:100452256..100454865-chr7:100471094..100473854,2	K562	blood:
8	chr7:100470857..100473840-chr8:103875332..103878147,2	K562	blood:
9	chr7:100422126..100425537-chr7:100471170..100475559,4	MCF-7	breast:
10	chr7:100471774..100474395-chr7:100608016..100610149,2	K562	blood:
11	chr7:100025223..100027930-chr7:100471250..100474138,3	MCF-7	breast:
12	chr7:100473070..100473992-chrX:24456211..24456942,2	MCF-7	breast:
13	chr7:100284400..100287604-chr7:100471903..100474319,4	MCF-7	breast:
14	chr1:11967269..11969054-chr7:100472288..100474008,2	MCF-7	breast:
15	chr7:100471473..100474219-chr7:100797756..100799384,2	MCF-7	breast:
16	chr15:65588153..65589893-chr7:100472867..100474526,2	MCF-7	breast:
17	chr7:100174947..100176871-chr7:100473137..100474758,2	K562	blood:
18	chr7:100448750..100454655-chr7:100469427..100474218,6	MCF-7	breast:
19	chr7:100181643..100184250-chr7:100471958..100474283,2	MCF-7	breast:
20	chr7:100025253..100027906-chr7:100472891..100474745,2	K562	blood:
21	chr7:100472601..100475489-chr7:100805185..100810298,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000253320	Chromatin interaction
ENSG00000225946	Chromatin interaction
ENSG00000146828	Chromatin interaction
ENSG00000196411	Chromatin interaction
ENSG00000146830	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000106336	Chromatin interaction
ENSG00000236305	Chromatin interaction
ENSG00000172336	Chromatin interaction
ENSG00000169894	Chromatin interaction
ENSG00000128564	Chromatin interaction
ENSG00000155096	Chromatin interaction
ENSG00000199568	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000077454	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000106367	Chromatin interaction
ENSG00000187514	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1054391	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11973000	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12666785	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12669120	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12672665	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705094	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12705097	0.87[EUR][1000 genomes]
rs13225631	0.85[EUR][1000 genomes]
rs13226043	0.98[ASN][1000 genomes]
rs13232524	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13240020	0.86[EUR][1000 genomes]
rs13241786	0.89[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs15624	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1799806	0.87[EUR][1000 genomes]
rs2405973	0.91[EUR][1000 genomes]
rs2405974	0.90[EUR][1000 genomes]
rs2405975	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2571598	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28852509	0.85[EUR][1000 genomes]
rs2894713	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3087504	0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs314329	0.81[EUR][1000 genomes]
rs314332	0.84[ASN][1000 genomes]
rs314369	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs314371	0.96[ASN][1000 genomes]
rs314372	0.93[ASN][1000 genomes]
rs314374	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs314375	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs314376	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs314377	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs314378	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34005963	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3757869	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3757870	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3757871	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3843541	0.85[EUR][1000 genomes]
rs3843542	0.88[EUR][1000 genomes]
rs3847063	0.96[CEU][hapmap]
rs3847064	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3847068	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3931823	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4727469	0.96[CEU][hapmap]
rs4729615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4729616	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap]
rs4729618	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs4729619	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4729620	0.96[CEU][hapmap]
rs6465776	0.83[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6942607	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6954151	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6976053	0.92[CEU][hapmap]
rs7783457	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7783543	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7798613	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7801015	0.98[ASN][1000 genomes]
rs7803865	0.96[CEU][hapmap]
rs9718841	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv1020837	chr7:100313122-100508635	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	nsv464647	chr7:100374087-100497131	Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv607965	chr7:100374087-100497131	Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv1032673	chr7:100382250-100606794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
9	nsv888797	chr7:100386900-100482026	Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
10	nsv888799	chr7:100406144-100497131	Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv888801	chr7:100416250-100497131	Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
12	nsv464648	chr7:100422156-100518458	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
13	nsv607966	chr7:100422156-100518458	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
14	nsv831073	chr7:100425659-100544888	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4729617	SHFM1	cis	cerebellum	SCAN
rs4729617	PLOD3	cis	cerebellum	SCAN
rs4729617	ZNF3	cis	parietal	SCAN
rs4729617	C7orf59	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100471400-100474800	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr7:100471600-100474000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr7:100471800-100473800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:100471800-100474000	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr7:100471800-100474200	Active TSS	H1 Cell Line	embryonic stem cell
6	chr7:100471800-100474200	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr7:100471800-100474400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr7:100472000-100473800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr7:100472000-100473800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr7:100472000-100473800	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr7:100472000-100473800	Active TSS	Fetal Kidney	kidney
12	chr7:100472000-100473800	Active TSS	Right Atrium	heart
13	chr7:100472000-100474000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:100472000-100474200	Active TSS	H9 Cell Line	embryonic stem cell
15	chr7:100472000-100474200	Active TSS	Psoas Muscle	Psoas
16	chr7:100472000-100474400	Active TSS	HSMMtube	muscle
17	chr7:100472200-100473800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:100472200-100473800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr7:100472200-100473800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr7:100472200-100473800	Active TSS	Brain Hippocampus Middle	brain
21	chr7:100472200-100473800	Active TSS	Esophagus	oesophagus
22	chr7:100472200-100474000	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr7:100472200-100474000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr7:100472200-100474000	Active TSS	A549	lung
25	chr7:100472200-100474200	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr7:100472200-100474200	Active TSS	HSMM	muscle
27	chr7:100472400-100473800	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr7:100472400-100474000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr7:100472400-100474000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr7:100472400-100474000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr7:100472400-100474000	Active TSS	Muscle Satellite Cultured Cells	--
32	chr7:100472400-100474000	Active TSS	GM12878-XiMat	blood
33	chr7:100472400-100474000	Active TSS	Hela-S3	cervix
34	chr7:100472400-100474000	Active TSS	Osteobl	bone
35	chr7:100472400-100474200	Active TSS	NHDF-Ad	bronchial
36	chr7:100472600-100474000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr7:100472600-100474000	Active TSS	HMEC	breast
38	chr7:100472800-100473800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
39	chr7:100472800-100474200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr7:100473000-100473800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr7:100473000-100474200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr7:100473200-100473800	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr7:100473200-100473800	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr7:100473200-100473800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr7:100473200-100473800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr7:100473200-100473800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr7:100473200-100473800	Flanking Active TSS	Brain Angular Gyrus	brain
48	chr7:100473200-100473800	Flanking Active TSS	Brain Cingulate Gyrus	brain
49	chr7:100473200-100473800	Flanking Active TSS	Placenta	Placenta
50	chr7:100473200-100473800	Flanking Active TSS	Left Ventricle	heart

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