Variant report

Variant	rs463901
Chromosome Location	chr5:178644294-178644295
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	chr5:178637418..178640045-chr5:178643551..178645345,3	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11740803	0.83[ASN][1000 genomes]
rs11744583	1.00[JPT][hapmap]
rs11747646	0.91[ASN][1000 genomes]
rs11750433	0.86[ASN][1000 genomes]
rs1614228	0.88[ASN][1000 genomes]
rs173072	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs180045	0.86[ASN][1000 genomes]
rs189255	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs191415	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2174971	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2457099	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs337805	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs389558	0.84[ASN][1000 genomes]
rs442406	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs455655	0.84[ASN][1000 genomes]
rs457187	0.91[ASN][1000 genomes]
rs458083	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs458272	0.91[ASN][1000 genomes]
rs459490	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs459668	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs461898	0.85[CEU][hapmap]
rs462646	0.84[ASN][1000 genomes]
rs463435	0.89[CEU][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs463455	0.84[ASN][1000 genomes]
rs463490	0.91[ASN][1000 genomes]
rs464156	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs464536	0.85[ASN][1000 genomes]
rs465381	0.91[ASN][1000 genomes]
rs465621	0.82[CHD][hapmap]
rs466363	0.91[ASN][1000 genomes]
rs466750	1.00[JPT][hapmap]
rs466752	0.83[ASN][1000 genomes]
rs467320	0.91[ASN][1000 genomes]
rs467333	0.91[ASN][1000 genomes]
rs592971	0.91[ASN][1000 genomes]
rs59887135	0.91[ASN][1000 genomes]
rs60819052	0.91[ASN][1000 genomes]
rs652766	0.86[ASN][1000 genomes]
rs662407	0.91[ASN][1000 genomes]
rs67436679	0.91[ASN][1000 genomes]
rs675880	0.91[ASN][1000 genomes]
rs73329780	0.81[ASN][1000 genomes]
rs7704451	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs7704836	0.89[CEU][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7718805	1.00[JPT][hapmap]
rs7734402	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024560	chr5:178415364-178917595	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv537975	chr5:178415364-178917595	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv1033597	chr5:178423101-178752095	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS 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	10 gene(s)	inside rSNPs	diseases
5	nsv1031829	chr5:178442633-178658706	Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv482750	chr5:178482653-178663586	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers 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	6 gene(s)	inside rSNPs	diseases
7	nsv1026790	chr5:178511268-178687428	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv482352	chr5:178525060-178697496	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1016097	chr5:178544084-178866001	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1026968	chr5:178545479-178865895	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv537976	chr5:178545479-178865895	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv600496	chr5:178552518-178752351	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv883226	chr5:178604465-178645310	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv883227	chr5:178604465-178659691	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv883228	chr5:178604465-178796142	Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	nsv883230	chr5:178614867-178648369	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv883231	chr5:178614867-178813207	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
18	nsv830558	chr5:178624391-178805604	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv883232	chr5:178626437-178805612	Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv1018641	chr5:178627012-178911254	ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
21	nsv537978	chr5:178627012-178911254	Flanking Bivalent TSS/Enh Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
22	nsv462575	chr5:178639040-178686438	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv600497	chr5:178639040-178686438	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs463901	RUFY1	cis	cerebellum	SCAN
rs463901	UIMC1	cis	parietal	SCAN
rs463901	OR2Y1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178619800-178650200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:178620200-178650200	Weak transcription	Fetal Lung	lung
3	chr5:178631800-178649800	Weak transcription	Gastric	stomach
4	chr5:178636600-178645000	Weak transcription	Spleen	Spleen
5	chr5:178637000-178645000	Weak transcription	Adipose Nuclei	Adipose
6	chr5:178637400-178644600	Weak transcription	Fetal Stomach	stomach
7	chr5:178638000-178644600	Weak transcription	HSMM	muscle
8	chr5:178638200-178656600	Weak transcription	HSMMtube	muscle
9	chr5:178638800-178647000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:178640600-178645000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:178640600-178645800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:178642400-178645200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:178642600-178645800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:178642800-178645400	Enhancers	NHDF-Ad	bronchial
15	chr5:178643000-178646200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:178643800-178646200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:178644000-178644600	Enhancers	Placenta Amnion	Placenta Amnion
18	chr5:178644000-178645200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr5:178644000-178645200	Enhancers	Osteobl	bone
20	chr5:178644000-178646200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:178644200-178645000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:178644200-178645400	Enhancers	NHLF	lung
23	chr5:178644200-178646000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:178644200-178654200	Weak transcription	Stomach Smooth Muscle	stomach

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