Variant report

Variant	rs7677289
Chromosome Location	chr4:91065352-91065353
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:91062775..91065678-chr4:91069290..91071948,2	MCF-7	breast:
2	chr4:91047815..91052213-chr4:91059218..91065616,9	MCF-7	breast:
3	chr4:91051066..91053200-chr4:91063053..91065601,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184305	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11932400	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11934796	0.99[ASN][1000 genomes]
rs11935738	0.99[ASN][1000 genomes]
rs11937976	0.99[ASN][1000 genomes]
rs11944177	0.99[ASN][1000 genomes]
rs11945007	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11947949	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11947970	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12331460	0.96[ASN][1000 genomes]
rs12644131	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12645259	0.99[ASN][1000 genomes]
rs12650984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13116571	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17016540	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs17016560	0.99[ASN][1000 genomes]
rs17016562	0.99[ASN][1000 genomes]
rs17016565	0.99[ASN][1000 genomes]
rs17016575	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17016581	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17016596	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17016622	0.95[ASN][1000 genomes]
rs1835518	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1835519	0.99[ASN][1000 genomes]
rs1835522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1835523	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.99[ASN][1000 genomes]
rs1835524	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1946567	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1963874	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1986976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2726	0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2870040	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35545901	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4339173	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4403004	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5006831	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55924200	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56054231	0.99[ASN][1000 genomes]
rs57291587	0.99[ASN][1000 genomes]
rs57711133	0.96[ASN][1000 genomes]
rs60047025	0.97[ASN][1000 genomes]
rs60520837	0.99[ASN][1000 genomes]
rs61308573	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61394011	0.99[ASN][1000 genomes]
rs6532214	0.99[ASN][1000 genomes]
rs6532215	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824746	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6829376	0.95[ASN][1000 genomes]
rs6834950	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6837278	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6838176	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72874369	0.91[EUR][1000 genomes]
rs72874395	0.99[ASN][1000 genomes]
rs72874402	0.99[ASN][1000 genomes]
rs72876108	0.99[ASN][1000 genomes]
rs72876110	0.98[ASN][1000 genomes]
rs72876113	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72876151	0.95[ASN][1000 genomes]
rs7667087	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7680617	0.99[ASN][1000 genomes]
rs7698120	0.95[ASN][1000 genomes]
rs9307081	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv470053	chr4:90879613-91439573	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv879537	chr4:90883047-91165346	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv931074	chr4:90970476-91753697	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv830006	chr4:90971656-91186340	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv879538	chr4:90993172-91080308	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv879539	chr4:91015463-91065352	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	nsv1007826	chr4:91049593-91438961	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv537177	chr4:91049593-91438961	Bivalent/Poised TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv999065	chr4:91049593-91520073	Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7677289	MMRN1	cis	parietal	SCAN
rs7677289	C4orf36	cis	cerebellum	SCAN
rs7677289	MMRN1	cis	cerebellum	SCAN
rs7677289	TSGA10	trans	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:91063600-91066000	Weak transcription	Brain Germinal Matrix	brain
2	chr4:91063800-91065400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:91063800-91067800	Weak transcription	Fetal Intestine Small	intestine
4	chr4:91063800-91069800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:91064400-91067400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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