Variant report

Variant	rs7698627
Chromosome Location	chr4:78774181-78774182
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	chr4:78740459..78743070-chr4:78773360..78775047,2	MCF-7	breast:
2	chr4:78739551..78742263-chr4:78772106..78775296,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138767	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10033527	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10033613	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097938	0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.94[ASN][1000 genomes]
rs11728886	0.82[ASN][1000 genomes]
rs11729215	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12645742	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13101418	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13101987	0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs13103035	0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[ASN][1000 genomes]
rs13103523	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13104947	0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs13106067	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13119606	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13120272	0.82[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.90[ASN][1000 genomes]
rs16996915	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.91[ASN][1000 genomes]
rs17002849	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2088992	0.89[JPT][hapmap]
rs2134050	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28404443	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28855210	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34830788	0.89[ASN][1000 genomes]
rs35648590	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35735677	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35979107	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4453957	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4571357	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4577601	0.95[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4859509	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859511	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859875	0.83[ASN][1000 genomes]
rs4859877	0.91[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4859879	0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.92[ASN][1000 genomes]
rs4859888	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859889	0.95[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62302728	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62302732	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6533282	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6533291	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6533344	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6533345	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66825464	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6811736	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6814912	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6848029	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6854895	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7670157	0.86[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7675009	0.86[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7676660	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs905376	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879501	chr4:78647634-78866007	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv1818157	chr4:78678104-78849088	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2752050	chr4:78693311-78975321	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1010714	chr4:78742505-78991030	Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv1824966	chr4:78747771-78823070	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv516836	chr4:78748977-78981919	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv594704	chr4:78748977-78981919	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv461562	chr4:78757015-78981919	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv461563	chr4:78757015-78981919	Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv594705	chr4:78757015-78981919	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7698627	MRPL1	cis	lymphoblastoid	seeQTL
rs7698627	FRAS1	cis	parietal	SCAN
rs7698627	C4orf26	cis	parietal	SCAN
rs7698627	MRPL1	cis	multi-tissue	Pritchard
rs7698627	MRPL1	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78765600-78775600	Weak transcription	NHEK	skin
2	chr4:78771200-78775400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:78771400-78775200	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:78773000-78774200	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr4:78773000-78774200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr4:78773400-78774200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr4:78773600-78774200	Enhancers	Thymus	Thymus
8	chr4:78773600-78774400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr4:78773600-78774400	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr4:78773600-78774800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:78773600-78775600	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr4:78773600-78776400	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr4:78773600-78779000	Enhancers	Primary B cells from peripheral blood	blood
14	chr4:78773800-78774200	Enhancers	Primary hematopoietic stem cells	blood
15	chr4:78773800-78775600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr4:78773800-78776400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr4:78773800-78776400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr4:78773800-78778600	Enhancers	Primary B cells from cord blood	blood
19	chr4:78774000-78774200	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr4:78774000-78774400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
21	chr4:78774000-78774400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
22	chr4:78774000-78774600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
23	chr4:78774000-78774600	Flanking Active TSS	Dnd41	blood
24	chr4:78774000-78774600	Enhancers	GM12878-XiMat	blood
25	chr4:78774000-78774800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr4:78774000-78775200	Weak transcription	Adipose Nuclei	Adipose
27	chr4:78774000-78775600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr4:78774000-78776400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr4:78774000-78776400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:78774000-78776400	Enhancers	Fetal Thymus	thymus
31	chr4:78774000-78776800	Enhancers	Primary monocytes fromperipheralblood	blood

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