Variant report

Variant	rs12035960
Chromosome Location	chr1:171615206-171615207
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171614558..171616177-chr1:171708966..171711154,2	MCF-7	breast:
2	chr1:171614465..171616509-chr1:171619659..171622072,2	MCF-7	breast:
3	chr1:171614371..171616986-chr1:171628195..171631368,3	K562	blood:
4	chr1:171613352..171616352-chr1:171748530..171751285,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010165	Chromatin interaction
ENSG00000034971	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10913388	1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12035719	0.92[CEU][hapmap];0.89[CHB][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1490185	0.92[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2236875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41263716	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57118325	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6425363	0.90[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7523603	1.00[CEU][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7527743	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7543786	0.84[CHB][hapmap];0.92[CHD][hapmap]
rs7547721	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555318	0.86[EUR][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	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS 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 miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171611400-171615800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:171613000-171616200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:171613600-171615600	Enhancers	Liver	Liver
4	chr1:171613800-171615400	Enhancers	Fetal Stomach	stomach
5	chr1:171614000-171615400	Enhancers	Brain Angular Gyrus	brain
6	chr1:171614000-171615400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:171614000-171615400	Enhancers	Fetal Muscle Leg	muscle
8	chr1:171614000-171615400	Enhancers	Placenta	Placenta
9	chr1:171614000-171615400	Enhancers	Ovary	ovary
10	chr1:171614000-171615400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr1:171614000-171615400	Enhancers	HSMMtube	muscle
12	chr1:171614000-171615400	Enhancers	NHLF	lung
13	chr1:171614000-171615400	Enhancers	Osteobl	bone
14	chr1:171614200-171615400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr1:171614200-171615400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:171614200-171615400	Enhancers	Left Ventricle	heart
17	chr1:171614200-171615400	Enhancers	HSMM	muscle
18	chr1:171614200-171615600	Enhancers	Fetal Heart	heart
19	chr1:171614200-171619000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:171614400-171615400	Enhancers	Aorta	Aorta
21	chr1:171614400-171615400	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr1:171614400-171615400	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr1:171614400-171615400	Enhancers	Psoas Muscle	Psoas
24	chr1:171614600-171615400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:171614600-171615600	Enhancers	NHDF-Ad	bronchial
26	chr1:171614600-171616200	Enhancers	Muscle Satellite Cultured Cells	--
27	chr1:171614600-171624600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:171615000-171615400	Enhancers	Fetal Muscle Trunk	muscle
29	chr1:171615000-171615600	Enhancers	Rectal Smooth Muscle	rectum
30	chr1:171615000-171616200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:171615000-171616400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:171615200-171615400	Enhancers	Adipose Nuclei	Adipose
33	chr1:171615200-171615400	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr1:171615200-171615400	Active TSS	Stomach Smooth Muscle	stomach
35	chr1:171615200-171615600	Enhancers	Colon Smooth Muscle	Colon
36	chr1:171615200-171623600	Weak transcription	Right Atrium	heart

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