Variant report

Variant	rs12143246
Chromosome Location	chr1:224864773-224864774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224863910..224865687-chr1:224877704..224880301,2	K562	blood:
2	chr1:224863922..224865503-chr1:224866664..224869416,2	K562	blood:
3	chr1:224855725..224858424-chr1:224861693..224865201,3	K562	blood:
4	chr1:224840003..224842948-chr1:224864305..224866677,2	MCF-7	breast:
5	chr1:224859647..224863135-chr1:224864370..224868600,5	K562	blood:

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

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

rs_ID	r²[population]
rs1004222	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10495226	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915688	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12117838	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12118368	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12122421	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12124222	1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12125381	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12130632	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12135641	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12136378	1.00[CEU][hapmap]
rs12136553	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12137592	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12139845	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12143128	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12143215	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16850250	1.00[YRI][hapmap]
rs16852009	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16852027	0.90[AMR][1000 genomes]
rs16852032	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16852083	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16852090	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2405527	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4360496	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5002414	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55927231	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56311342	0.82[EUR][1000 genomes]
rs6666956	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6672460	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6685335	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6685547	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6694298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6694864	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6695061	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6695253	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6695579	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6696394	0.86[AMR][1000 genomes]
rs879363	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]

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:19 , 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	chr1:224832800-224869000	Weak transcription	Dnd41	blood
3	chr1:224833200-224874400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:224857200-224869000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:224857200-224869200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:224858400-224871800	Weak transcription	NHLF	lung
7	chr1:224858400-224874200	Weak transcription	NH-A	brain
8	chr1:224859600-224871400	Weak transcription	NHDF-Ad	bronchial
9	chr1:224861200-224865200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:224861200-224876800	Weak transcription	Ovary	ovary
11	chr1:224862400-224865200	Weak transcription	Right Atrium	heart
12	chr1:224862400-224902000	Weak transcription	Pancreas	Pancrea
13	chr1:224862800-224869400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:224864000-224876200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:224864200-224865800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:224864200-224866400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:224864400-224864800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:224864600-224869000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:224864600-224871600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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