Variant report

Variant	rs904272
Chromosome Location	chr1:179779798-179779799
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179672208..179674210-chr1:179778316..179781099,2	MCF-7	breast:
2	chr1:179674246..179676441-chr1:179778955..179781367,2	MCF-7	breast:
3	chr1:179675218..179676600-chr1:179778027..179780620,16	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1148824	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1281422	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236589	0.88[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2647226	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2777920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794588	0.82[CEU][hapmap]
rs2794589	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3845386	0.84[CEU][hapmap]
rs4320747	0.84[CEU][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6425594	0.88[CEU][hapmap]
rs6658638	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6684425	0.92[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6690639	0.85[CEU][hapmap]
rs6695329	0.89[CEU][hapmap]
rs6701652	0.81[CEU][hapmap]
rs7552673	0.87[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	nsv1009961	chr1:179714247-179790110	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1011407	chr1:179733193-179799430	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv520418	chr1:179761601-179794602	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv519307	chr1:179766086-179795505	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179777000-179781600	Enhancers	Fetal Thymus	thymus
2	chr1:179777200-179783600	Weak transcription	Right Atrium	heart
3	chr1:179778400-179780000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr1:179778600-179779800	Enhancers	Fetal Muscle Trunk	muscle
5	chr1:179778600-179779800	Bivalent Enhancer	Fetal Muscle Leg	muscle
6	chr1:179778800-179779800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:179779000-179779800	Bivalent Enhancer	Fetal Stomach	stomach
8	chr1:179779000-179779800	Enhancers	HMEC	breast
9	chr1:179779000-179781200	Weak transcription	Brain Germinal Matrix	brain
10	chr1:179779000-179781600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:179779000-179783400	Weak transcription	Esophagus	oesophagus
12	chr1:179779200-179779800	Bivalent Enhancer	NHEK	skin
13	chr1:179779200-179780000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:179779200-179781400	Weak transcription	Fetal Intestine Small	intestine
15	chr1:179779200-179783200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:179779200-179783200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr1:179779200-179783200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:179779200-179783200	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:179779200-179783400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:179779200-179783400	Weak transcription	Brain Angular Gyrus	brain
21	chr1:179779200-179783400	Weak transcription	Brain Anterior Caudate	brain
22	chr1:179779200-179783400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:179779200-179783400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:179779200-179783400	Weak transcription	Brain Substantia Nigra	brain
25	chr1:179779200-179783400	Weak transcription	Fetal Intestine Large	intestine
26	chr1:179779200-179783600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:179779200-179783600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:179779400-179779800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:179779600-179779800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:179779600-179779800	Bivalent Enhancer	Placenta	Placenta

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