Variant report

Variant	rs9861978
Chromosome Location	chr3:118686299-118686300
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	chr3:118683148..118684956-chr3:118685063..118686921,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10934470	0.89[JPT][hapmap]
rs12491833	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1369580	0.89[JPT][hapmap]
rs1369581	0.88[JPT][hapmap]
rs1369582	0.89[JPT][hapmap]
rs1435662	0.89[JPT][hapmap]
rs1435667	0.89[JPT][hapmap]
rs4687835	0.89[JPT][hapmap]
rs4687959	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6438481	0.87[JPT][hapmap]
rs6773729	0.82[EUR][1000 genomes]
rs6786886	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792805	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7613076	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7641626	0.89[JPT][hapmap]
rs9289117	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9824063	0.87[ASN][1000 genomes]
rs9872674	0.89[JPT][hapmap]
rs9878706	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv1010475	chr3:118657382-118789714	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv877369	chr3:118681771-118824418	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118679000-118688200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:118680200-118686600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr3:118680200-118686600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr3:118680200-118688200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:118680200-118688200	Weak transcription	Ovary	ovary
6	chr3:118681200-118694000	Enhancers	Brain Substantia Nigra	brain
7	chr3:118681400-118690000	Enhancers	Brain Hippocampus Middle	brain
8	chr3:118681800-118692800	Enhancers	Brain Anterior Caudate	brain
9	chr3:118683400-118696200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:118683800-118689000	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr3:118684000-118687400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr3:118684400-118690000	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr3:118684600-118687600	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr3:118684600-118690200	Enhancers	Brain Cingulate Gyrus	brain
15	chr3:118684800-118687600	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr3:118684800-118690200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:118684800-118694000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr3:118685000-118688800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:118685000-118690000	Enhancers	Brain Angular Gyrus	brain
20	chr3:118685400-118686400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:118685400-118689400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:118685800-118686800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:118685800-118687800	Weak transcription	Right Atrium	heart
24	chr3:118685800-118688200	Weak transcription	Psoas Muscle	Psoas
25	chr3:118685800-118688400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:118686000-118687600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr3:118686200-118687600	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr3:118686200-118689000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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