Variant report

Variant	rs10513557
Chromosome Location	chr3:160594496-160594497
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	chr3:160471557..160473461-chr3:160592163..160595089,2	K562	blood:

Variant related genes	Relation type
ENSG00000260572	Chromatin interaction
ENSG00000163590	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10513561	1.00[CHD][hapmap]
rs10513563	1.00[CEU][hapmap]
rs12486103	1.00[CHB][hapmap]
rs12486691	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12487156	1.00[CHD][hapmap]
rs12488403	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12492000	0.84[EUR][1000 genomes]
rs12492376	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12630250	1.00[CEU][hapmap]
rs1374792	1.00[CEU][hapmap]
rs1447612	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1447613	1.00[CEU][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs16831546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16831549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831552	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831555	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16831611	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][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];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16831760	1.00[CEU][hapmap]
rs16831771	1.00[CEU][hapmap]
rs16831799	0.82[CHB][hapmap]
rs16831802	1.00[CEU][hapmap]
rs16831864	0.82[CHB][hapmap]
rs17405707	1.00[CEU][hapmap]
rs3925722	0.82[CHB][hapmap]
rs58693796	0.91[ASN][1000 genomes]
rs59252183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59647128	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6441341	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6441350	0.82[CHB][hapmap]
rs6787599	0.85[CEU][hapmap];1.00[CHB][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]
rs6790705	1.00[CHB][hapmap]
rs6796168	0.82[CHB][hapmap]
rs6800309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6806729	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs6807796	1.00[CEU][hapmap];1.00[CHB][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]
rs7627500	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs935499	1.00[CEU][hapmap];1.00[CHB][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]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv32963	chr3:160555238-160603116	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160589000-160596000	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:160591800-160595600	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr3:160592200-160595600	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr3:160593600-160594600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:160593600-160594600	Enhancers	Brain Substantia Nigra	brain
6	chr3:160593600-160594800	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr3:160593600-160594800	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr3:160593600-160595000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:160593600-160595000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:160593600-160595000	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr3:160594000-160594600	Enhancers	Brain Angular Gyrus	brain
12	chr3:160594000-160594600	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr3:160594000-160594600	Enhancers	Fetal Heart	heart
14	chr3:160594000-160594600	Enhancers	Right Atrium	heart
15	chr3:160594000-160594800	Enhancers	Brain Anterior Caudate	brain
16	chr3:160594000-160594800	Enhancers	Brain Cingulate Gyrus	brain
17	chr3:160594000-160594800	Enhancers	Brain Hippocampus Middle	brain
18	chr3:160594000-160594800	Enhancers	Fetal Muscle Leg	muscle
19	chr3:160594000-160594800	Enhancers	Left Ventricle	heart
20	chr3:160594000-160595000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:160594000-160595400	Enhancers	Psoas Muscle	Psoas
22	chr3:160594200-160595200	Enhancers	Stomach Smooth Muscle	stomach
23	chr3:160594400-160594600	Enhancers	Right Ventricle	heart
24	chr3:160594400-160595000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:160594400-160595000	Enhancers	Liver	Liver

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