Variant report

Variant	rs12121072
Chromosome Location	chr1:171187784-171187785
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	chr1:171182864..171185763-chr1:171186408..171189341,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10912667	0.89[ASN][1000 genomes]
rs12124505	1.00[ASN][1000 genomes]
rs12126946	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2020870	0.81[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2072756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075989	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];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28369802	0.86[ASN][1000 genomes]
rs28369803	0.86[ASN][1000 genomes]
rs28369818	0.90[ASN][1000 genomes]
rs28369863	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28369865	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28369918	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28384819	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662994	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6662995	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7518693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7519117	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7527067	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527478	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7539639	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7542361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7551282	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	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
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12121072	FMO2	cis	parietal	SCAN
rs12121072	GPR161	cis	cerebellum	SCAN
rs12121072	RCSD1	cis	cerebellum	SCAN
rs12121072	FMO3	cis	cerebellum	SCAN
rs12121072	KIFAP3	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171167200-171187800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr1:171169800-171189800	Weak transcription	Right Atrium	heart
3	chr1:171179800-171187800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:171181000-171187800	Weak transcription	Fetal Lung	lung
5	chr1:171182800-171187800	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:171183000-171189800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:171183400-171189800	Weak transcription	Left Ventricle	heart
8	chr1:171183600-171187800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:171184000-171187800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:171184200-171187800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:171185400-171189000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:171185800-171189200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr1:171186600-171189000	Enhancers	NHEK	skin
14	chr1:171186600-171189200	Enhancers	HMEC	breast
15	chr1:171186800-171188800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr1:171186800-171189200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:171186800-171189600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:171186800-171190200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:171186800-171190200	Enhancers	Placenta	Placenta
20	chr1:171187000-171188000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
21	chr1:171187000-171189200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr1:171187200-171188000	Enhancers	Aorta	Aorta
23	chr1:171187200-171188000	Enhancers	Fetal Muscle Trunk	muscle
24	chr1:171187200-171188000	Enhancers	Gastric	stomach
25	chr1:171187200-171188800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr1:171187200-171189600	Enhancers	Adipose Nuclei	Adipose
27	chr1:171187200-171190400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:171187400-171187800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:171187400-171188000	Enhancers	Fetal Muscle Leg	muscle
30	chr1:171187400-171188600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:171187400-171188800	Enhancers	Muscle Satellite Cultured Cells	--
32	chr1:171187400-171189800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:171187600-171187800	Weak transcription	Psoas Muscle	Psoas
34	chr1:171187600-171188000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:171187600-171188000	Enhancers	Pancreas	Pancrea
36	chr1:171187600-171188800	Enhancers	Brain Substantia Nigra	brain
37	chr1:171187600-171189200	Enhancers	Osteobl	bone
38	chr1:171187600-171189400	Enhancers	Fetal Stomach	stomach
39	chr1:171187600-171189600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:171187600-171190400	Enhancers	Stomach Mucosa	stomach

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