Variant report

Variant	rs16859871
Chromosome Location	chr3:112351676-112351677
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112338141..112343361-chr3:112351475..112354709,4	MCF-7	breast:
2	chr3:112344415..112347197-chr3:112350553..112352868,2	K562	blood:
3	chr3:112350080..112353120-chr3:112708595..112712214,3	K562	blood:
4	chr3:112346448..112348470-chr3:112351397..112354527,3	K562	blood:
5	chr3:112346979..112353983-chr3:112357134..112359925,9	K562	blood:

Variant related genes	Relation type
ENSG00000163607	Chromatin interaction
ENSG00000091986	Chromatin interaction
ENSG00000272844	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10934178	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10934179	0.86[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11711357	1.00[YRI][hapmap]
rs11712917	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1388443	0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16859870	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3732817	1.00[YRI][hapmap]
rs4682418	0.86[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7349537	0.87[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7349538	0.91[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9288953	1.00[YRI][hapmap]
rs9288955	0.86[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9831088	1.00[YRI][hapmap]
rs9833212	0.86[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9851689	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9855848	1.00[YRI][hapmap]
rs9861342	0.83[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9870432	0.86[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9881785	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112331400-112354800	Weak transcription	Psoas Muscle	Psoas
2	chr3:112336600-112355800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:112342600-112359600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:112343400-112358000	Weak transcription	Pancreas	Pancrea
5	chr3:112345000-112353800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr3:112345200-112359400	Weak transcription	Esophagus	oesophagus
7	chr3:112346200-112352400	Weak transcription	Brain Anterior Caudate	brain
8	chr3:112346200-112352400	Weak transcription	Fetal Brain Female	brain
9	chr3:112346400-112354000	Weak transcription	Fetal Heart	heart
10	chr3:112346600-112353800	Weak transcription	Aorta	Aorta
11	chr3:112347800-112353200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:112348000-112353200	Enhancers	Rectal Smooth Muscle	rectum
13	chr3:112348200-112351800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr3:112348200-112351800	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr3:112348200-112358400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:112348600-112357200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:112348800-112353800	Weak transcription	GM12878-XiMat	blood
18	chr3:112348800-112358400	Weak transcription	Hela-S3	cervix
19	chr3:112349000-112351800	Weak transcription	HMEC	breast
20	chr3:112349000-112351800	Weak transcription	NHEK	skin
21	chr3:112349000-112354400	Enhancers	A549	lung
22	chr3:112349200-112352200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:112349200-112354400	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:112350000-112353200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:112350000-112353600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:112350000-112354400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:112350000-112354600	Enhancers	H1 Cell Line	embryonic stem cell
28	chr3:112350000-112354600	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr3:112350000-112354600	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr3:112350200-112354400	Flanking Active TSS	NHDF-Ad	bronchial
31	chr3:112350800-112351800	Enhancers	HSMMtube	muscle
32	chr3:112351000-112352000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:112351200-112352200	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr3:112351200-112352800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:112351200-112353000	Flanking Active TSS	NHLF	lung
36	chr3:112351200-112353800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:112351200-112354000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:112351200-112355600	Enhancers	Fetal Kidney	kidney
39	chr3:112351400-112351800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr3:112351400-112351800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:112351400-112351800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr3:112351400-112351800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:112351400-112351800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:112351400-112351800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:112351400-112351800	Flanking Active TSS	Colon Smooth Muscle	Colon
46	chr3:112351400-112351800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr3:112351400-112352000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
48	chr3:112351400-112352000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:112351400-112352400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:112351400-112352600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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