Variant report

Variant	rs1577108
Chromosome Location	chr6:71423441-71423442
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:71422116..71424990-chr6:71593570..71595657,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10498874	0.85[MEX][hapmap]
rs10498876	0.81[MEX][hapmap]
rs10755541	0.85[MEX][hapmap]
rs10755543	0.81[MEX][hapmap]
rs1084388	0.85[MEX][hapmap]
rs10945243	0.85[MEX][hapmap]
rs10945246	0.81[MEX][hapmap]
rs10945247	0.81[MEX][hapmap]
rs12198750	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12202909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12203399	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];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12212629	0.85[MEX][hapmap]
rs12215757	0.85[MEX][hapmap]
rs12215835	0.81[MEX][hapmap]
rs13174	0.96[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1333966	1.00[ASW][hapmap]
rs1333967	0.81[MEX][hapmap]
rs1577110	0.85[MEX][hapmap]
rs1716007	0.85[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes]
rs17763188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1855437	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2347433	0.85[MEX][hapmap]
rs2460689	0.81[MEX][hapmap]
rs2474913	0.81[MEX][hapmap]
rs2474917	0.85[MEX][hapmap]
rs2504756	0.81[MEX][hapmap]
rs2504757	0.85[MEX][hapmap]
rs4613778	0.81[MEX][hapmap]
rs4706458	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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4706462	0.81[MEX][hapmap]
rs4706464	0.81[MEX][hapmap]
rs4707843	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4707847	0.80[MEX][hapmap]
rs4707851	0.85[MEX][hapmap]
rs4707854	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4707855	0.81[MEX][hapmap]
rs615526	0.83[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7451673	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7760267	0.81[MEX][hapmap]
rs7771674	0.81[MEX][hapmap]
rs781967	0.85[MEX][hapmap]
rs781968	0.85[MEX][hapmap]
rs781969	0.81[MEX][hapmap]
rs781977	0.81[MEX][hapmap]
rs781978	0.81[MEX][hapmap]
rs781982	0.81[MEX][hapmap]
rs781983	0.81[MEX][hapmap]
rs781987	0.81[MEX][hapmap]
rs781989	0.85[MEX][hapmap]
rs781990	0.81[MEX][hapmap]
rs9364097	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9455215	0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv886147	chr6:71273253-71471863	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS 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	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1577108	FAM135A	cis	cerebellum	SCAN
rs1577108	OGFRL1	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71418000-71423600	Weak transcription	Primary T cells from cord blood	blood
2	chr6:71418200-71426800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:71418400-71424400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:71419400-71424400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr6:71420000-71435200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr6:71420000-71436800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:71421600-71424800	Weak transcription	Aorta	Aorta
8	chr6:71422000-71435200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:71423000-71425400	ZNF genes & repeats	GM12878-XiMat	blood
10	chr6:71423000-71426600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:71423200-71426200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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