Variant report

Variant	rs12060624
Chromosome Location	chr1:120415364-120415365
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120283662..120285685-chr1:120414247..120416692,2	MCF-7	breast:
2	chr1:120356024..120358010-chr1:120414554..120416804,2	MCF-7	breast:
3	chr1:120414299..120416081-chr1:120419114..120421121,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10127888	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10923920	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10923931	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12057420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12061487	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12061529	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12097800	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1493694	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17024432	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17186372	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17258599	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2027447	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2453040	1.00[JPT][hapmap]
rs2453058	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2493389	1.00[JPT][hapmap]
rs2493391	1.00[JPT][hapmap]
rs2493392	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2493394	1.00[JPT][hapmap]
rs2641317	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2641346	1.00[JPT][hapmap]
rs2641352	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2793829	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2793831	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2843024	1.00[JPT][hapmap]
rs2934381	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2934387	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs327205	1.00[JPT][hapmap]
rs3897478	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3911328	1.00[JPT][hapmap]
rs60234477	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60949447	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61447698	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6668119	1.00[JPT][hapmap]
rs6669867	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67591840	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67765421	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67905606	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs699779	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7515431	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7534585	1.00[JPT][hapmap]
rs7534586	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs835575	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs835576	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9662844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv915933	chr1:120323527-120471049	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv831226	chr1:120331599-120471049	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv533996	chr1:120359524-120471049	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv436325	chr1:120390914-120471049	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120409600-120416000	Weak transcription	Fetal Lung	lung
2	chr1:120413400-120417200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:120413600-120417000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:120413800-120417200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:120413800-120417200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:120413800-120417200	Enhancers	HSMM	muscle
7	chr1:120413800-120417200	Enhancers	NHDF-Ad	bronchial
8	chr1:120413800-120417200	Enhancers	NHLF	lung
9	chr1:120413800-120417600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:120414000-120415400	Weak transcription	HSMMtube	muscle
11	chr1:120414200-120415600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:120414200-120415800	Weak transcription	K562	blood
13	chr1:120414200-120416400	Weak transcription	Adipose Nuclei	Adipose
14	chr1:120414200-120416800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:120414200-120417200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:120414200-120417200	Enhancers	Muscle Satellite Cultured Cells	--
17	chr1:120414200-120417200	Enhancers	Osteobl	bone
18	chr1:120414200-120419600	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr1:120414400-120415400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:120414400-120415400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:120414400-120415800	Weak transcription	Right Atrium	heart
22	chr1:120414400-120417000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:120414600-120419800	Weak transcription	Dnd41	blood
24	chr1:120415000-120417000	Enhancers	Fetal Kidney	kidney
25	chr1:120415000-120417200	Enhancers	Colon Smooth Muscle	Colon
26	chr1:120415000-120417200	Enhancers	Fetal Muscle Leg	muscle
27	chr1:120415200-120415600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:120415200-120415600	Enhancers	Fetal Muscle Trunk	muscle
29	chr1:120415200-120416000	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr1:120415200-120417000	Enhancers	Fetal Heart	heart
31	chr1:120415200-120417200	Enhancers	Fetal Stomach	stomach
32	chr1:120415200-120417200	Enhancers	Rectal Smooth Muscle	rectum
33	chr1:120415200-120417200	Enhancers	Stomach Smooth Muscle	stomach
34	chr1:120415200-120417200	Enhancers	HMEC	breast
35	chr1:120415200-120417200	Enhancers	NH-A	brain

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