Variant report

Variant	rs12060334
Chromosome Location	chr1:224869460-224869461
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	chr1:224869255..224871044-chr1:224877081..224878780,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1036431	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1039265	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10495227	0.85[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10915691	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10915693	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10915695	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1106233	0.83[CEU][hapmap]
rs11805320	0.81[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12058085	0.85[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12062831	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12065840	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12068125	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12072810	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12073052	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12077707	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12079156	0.84[EUR][1000 genomes]
rs12088524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12092532	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12096245	0.83[CEU][hapmap]
rs12562581	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12565092	0.84[EUR][1000 genomes]
rs12567125	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1337538	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1369848	0.80[EUR][1000 genomes]
rs1465766	0.92[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1465767	0.85[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1499289	0.83[CEU][hapmap]
rs1532557	0.83[CEU][hapmap]
rs16850786	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4363402	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61603030	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61827113	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61827152	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695864	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs7541279	0.92[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7554310	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs883116	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224832200-224884400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:224833200-224874400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:224858400-224871800	Weak transcription	NHLF	lung
4	chr1:224858400-224874200	Weak transcription	NH-A	brain
5	chr1:224859600-224871400	Weak transcription	NHDF-Ad	bronchial
6	chr1:224861200-224876800	Weak transcription	Ovary	ovary
7	chr1:224862400-224902000	Weak transcription	Pancreas	Pancrea
8	chr1:224864000-224876200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:224864600-224871600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:224867800-224872400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:224868000-224871800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:224868000-224874000	Weak transcription	Gastric	stomach
13	chr1:224868400-224875200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:224869000-224869800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:224869000-224869800	Strong transcription	Dnd41	blood
16	chr1:224869000-224870000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:224869200-224869600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:224869200-224870200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:224869200-224870200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:224869400-224869800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:224869400-224870000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:224869400-224870400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:224869400-224872600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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