Variant report

Variant	rs12729858
Chromosome Location	chr1:91842164-91842165
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:91841976..91844077-chr1:91877558..91879218,2	K562	blood:
2	chr1:91841748..91844457-chr1:91845517..91848039,2	K562	blood:
3	chr1:91840019..91844742-chr1:91867807..91870746,5	K562	blood:

Variant related genes	Relation type
ENSG00000162669	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12562039	0.88[AMR][1000 genomes]
rs12564415	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12567679	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap]
rs12567930	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12746156	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12756869	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12757442	0.81[AMR][1000 genomes]
rs12759453	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12760267	0.91[CEU][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17131418	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1974253	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2060997	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2099749	0.87[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28395174	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34105527	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34507721	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34600283	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34809593	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34840774	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35081855	0.85[AMR][1000 genomes]
rs35462750	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4248874	0.83[AMR][1000 genomes]
rs4658210	0.81[AMR][1000 genomes]
rs4658215	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66730201	0.87[AMR][1000 genomes]
rs920469	1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949516	chr1:91644418-92109261	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv1800676	chr1:91722083-91854389	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv1796351	chr1:91722083-91872374	Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv871685	chr1:91774458-91849219	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv546806	chr1:91780408-91875505	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:91819400-91845200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr1:91822800-91849000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:91824800-91852600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr1:91825000-91852600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:91829800-91852600	Weak transcription	Brain Germinal Matrix	brain
6	chr1:91832000-91852600	Weak transcription	Fetal Heart	heart
7	chr1:91833000-91852600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:91833000-91852600	Weak transcription	Fetal Stomach	stomach
9	chr1:91836800-91852600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:91837200-91846000	Weak transcription	Psoas Muscle	Psoas
11	chr1:91839000-91852600	Weak transcription	Fetal Intestine Large	intestine
12	chr1:91839800-91846600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:91840400-91852600	Weak transcription	Fetal Kidney	kidney
14	chr1:91840600-91852600	Weak transcription	Ovary	ovary
15	chr1:91840800-91852600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:91840800-91852600	Weak transcription	Fetal Brain Male	brain
17	chr1:91840800-91852600	Weak transcription	Fetal Lung	lung
18	chr1:91841200-91843000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:91841200-91847400	Weak transcription	Left Ventricle	heart
20	chr1:91841400-91852600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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