Variant report

Variant	rs6671398
Chromosome Location	chr1:153535509-153535510
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153535304..153546939-chr1:153598248..153612195,40	MCF-7	breast:
2	chr1:153533881..153554060-chr1:153575339..153590405,58	MCF-7	breast:
3	chr1:153532321..153535905-chr1:153536824..153539528,6	MCF-7	breast:
4	chr1:153534464..153536760-chr1:153538176..153540228,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189171	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000189334	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000188643	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1047325	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1050923	0.88[EUR][1000 genomes]
rs11488669	0.91[EUR][1000 genomes]
rs16835437	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16835455	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28452456	0.88[EUR][1000 genomes]
rs28548347	0.88[EUR][1000 genomes]
rs28594230	0.91[EUR][1000 genomes]
rs28689606	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28718953	0.88[EUR][1000 genomes]
rs36022742	0.88[EUR][1000 genomes]
rs3762268	0.94[EUR][1000 genomes]
rs41265162	0.88[EUR][1000 genomes]
rs41265164	0.88[EUR][1000 genomes]
rs4595398	0.88[EUR][1000 genomes]
rs55955983	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56043239	0.88[EUR][1000 genomes]
rs56057245	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56089062	0.88[EUR][1000 genomes]
rs56350425	0.88[EUR][1000 genomes]
rs56838169	0.88[EUR][1000 genomes]
rs57024596	0.88[EUR][1000 genomes]
rs58056804	0.91[EUR][1000 genomes]
rs58072118	0.88[EUR][1000 genomes]
rs59376279	0.88[EUR][1000 genomes]
rs60069797	1.00[ASN][1000 genomes]
rs60218214	0.94[EUR][1000 genomes]
rs60287468	0.91[EUR][1000 genomes]
rs61265945	0.88[EUR][1000 genomes]
rs61558997	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427301	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6700310	0.85[EUR][1000 genomes]
rs6702891	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6703014	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73026350	0.88[EUR][1000 genomes]
rs74115473	0.91[EUR][1000 genomes]
rs74115476	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8401	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
4	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153522600-153538000	Weak transcription	Colonic Mucosa	Colon
2	chr1:153527200-153536200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:153527200-153536400	Weak transcription	Spleen	Spleen
4	chr1:153527400-153535800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:153527400-153536200	Weak transcription	NHLF	lung
6	chr1:153527600-153536000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:153527600-153536200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:153532800-153539600	Weak transcription	Thymus	Thymus
9	chr1:153533800-153537400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:153533800-153537400	Transcr. at gene 5' and 3'	HMEC	breast
11	chr1:153533800-153537600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:153534000-153537800	Weak transcription	Fetal Lung	lung
13	chr1:153534200-153536600	Enhancers	Hela-S3	cervix
14	chr1:153534200-153537000	Weak transcription	HUVEC	blood vessel
15	chr1:153534200-153537400	Transcr. at gene 5' and 3'	NHEK	skin
16	chr1:153534400-153535800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:153534400-153536000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:153534400-153536000	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr1:153534400-153536000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr1:153534400-153536000	Weak transcription	Lung	lung
21	chr1:153534400-153536000	Weak transcription	A549	lung
22	chr1:153534400-153537800	Weak transcription	Ovary	ovary
23	chr1:153534400-153537800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:153534800-153536000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:153535200-153536000	Active TSS	Esophagus	oesophagus
26	chr1:153535200-153536800	Weak transcription	Stomach Mucosa	stomach
27	chr1:153535400-153538400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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