Variant report

Variant	rs9860173
Chromosome Location	chr3:118705089-118705090
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10488303	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11923277	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12491204	0.82[CHB][hapmap]
rs16829203	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16829206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17491031	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2866319	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41330049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41414745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41523948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56314531	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6785161	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6795523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9817851	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9836742	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9861721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862556	1.00[YRI][hapmap]
rs9882006	1.00[YRI][hapmap]

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	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
5	esv2756586	chr3:118688611-118863998	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118688800-118706000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:118699200-118706000	Enhancers	Brain Substantia Nigra	brain
3	chr3:118700200-118706200	Enhancers	Brain Hippocampus Middle	brain
4	chr3:118700400-118705800	Enhancers	Brain Cingulate Gyrus	brain
5	chr3:118700400-118706000	Enhancers	Brain Angular Gyrus	brain
6	chr3:118700400-118707800	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr3:118701000-118706200	Weak transcription	Psoas Muscle	Psoas
8	chr3:118701600-118709800	Enhancers	Brain Anterior Caudate	brain
9	chr3:118702200-118710600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:118703000-118707800	Enhancers	Fetal Heart	heart
11	chr3:118703200-118707400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr3:118703600-118705200	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr3:118703600-118705200	Enhancers	Right Atrium	heart
14	chr3:118703600-118707800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr3:118703600-118708200	Enhancers	Ovary	ovary
16	chr3:118703600-118710000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:118703800-118705200	Enhancers	K562	blood
18	chr3:118703800-118705800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:118703800-118706000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:118703800-118706200	Weak transcription	Left Ventricle	heart
21	chr3:118704200-118706600	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr3:118704200-118710000	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr3:118704400-118706000	Weak transcription	Fetal Brain Male	brain
24	chr3:118704400-118706600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:118704400-118707200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr3:118704400-118707600	Enhancers	Stomach Smooth Muscle	stomach
27	chr3:118704400-118710200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:118704600-118705200	Enhancers	H1 Cell Line	embryonic stem cell
29	chr3:118704600-118705200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:118704600-118707600	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr3:118704600-118707800	Enhancers	Brain Germinal Matrix	brain
32	chr3:118704800-118705200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:118704800-118705200	Enhancers	Placenta	Placenta
34	chr3:118704800-118705200	Enhancers	Pancreas	Pancrea
35	chr3:118704800-118706800	Enhancers	Colon Smooth Muscle	Colon
36	chr3:118704800-118707000	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr3:118704800-118707200	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr3:118705000-118706000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:118705000-118706400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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