Variant report

Variant	rs396797
Chromosome Location	chr3:155469798-155469799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:155463358..155465336-chr3:155469536..155471371,2	K562	blood:
2	chr3:155466610..155468263-chr3:155468525..155471754,3	MCF-7	breast:
3	chr3:155468097..155470070-chr3:155473602..155476572,2	K562	blood:
4	chr3:155467979..155469957-chr3:155586823..155589749,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163655	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10936015	0.80[AMR][1000 genomes]
rs11923772	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13060077	0.91[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs173370	0.81[AMR][1000 genomes]
rs17349784	0.91[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs184836	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2201932	0.91[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2320190	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34112296	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs35404700	0.81[ASN][1000 genomes]
rs35769564	0.92[AFR][1000 genomes]
rs358714	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs358720	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs358722	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs358734	0.83[JPT][hapmap]
rs358736	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs358738	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs358740	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs358741	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs358744	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs358745	1.00[CEU][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs358746	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs358748	0.92[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35963081	0.92[AFR][1000 genomes]
rs369155	0.92[ASN][1000 genomes]
rs400999	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs426236	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4680215	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680216	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs57183957	0.96[ASN][1000 genomes]
rs62284707	0.95[ASN][1000 genomes]
rs6441012	0.89[ASN][1000 genomes]
rs6774542	0.81[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs6794117	0.81[CHB][hapmap];0.91[YRI][hapmap]
rs7619505	0.81[AMR][1000 genomes]
rs7642920	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs9866823	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009618	chr3:155370034-155492177	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv829763	chr3:155417552-155470079	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv877680	chr3:155438022-155723064	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 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	chr3:155463800-155475200	Weak transcription	Left Ventricle	heart
2	chr3:155463800-155487800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:155463800-155501200	Weak transcription	Aorta	Aorta
4	chr3:155464000-155476600	Weak transcription	Ovary	ovary
5	chr3:155464200-155469800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:155464200-155474800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:155464200-155487600	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:155464200-155487600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:155464200-155487800	Weak transcription	Adipose Nuclei	Adipose
10	chr3:155464200-155487800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr3:155464200-155487800	Weak transcription	Pancreas	Pancrea
12	chr3:155464200-155489600	Weak transcription	Brain Anterior Caudate	brain
13	chr3:155464200-155490600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:155464600-155487800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:155466400-155484600	Weak transcription	Fetal Brain Male	brain
16	chr3:155467000-155487200	Weak transcription	Fetal Brain Female	brain
17	chr3:155467200-155469800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:155467200-155478400	Weak transcription	Fetal Intestine Large	intestine
19	chr3:155467200-155479400	Weak transcription	Fetal Intestine Small	intestine
20	chr3:155467200-155500200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:155467200-155508000	Weak transcription	K562	blood
22	chr3:155467200-155508800	Weak transcription	Hela-S3	cervix
23	chr3:155467400-155469800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:155467400-155470800	Weak transcription	A549	lung
25	chr3:155467400-155481600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:155467400-155508400	Weak transcription	HepG2	liver
27	chr3:155468000-155487200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:155469400-155481600	Weak transcription	Liver	Liver
29	chr3:155469600-155469800	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr3:155469600-155470000	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr3:155469600-155470200	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr3:155469600-155470400	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr3:155469600-155470400	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr3:155469600-155470400	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr3:155469600-155470400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:155469600-155470800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:155469600-155471000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:155469600-155471000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:155469600-155471000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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