Variant report

Variant	rs3816326
Chromosome Location	chr5:52396500-52396501
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:52388236..52391143-chr5:52395060..52396954,3	K562	blood:
2	chr5:52395727..52398298-chr5:52405224..52406865,2	MCF-7	breast:
3	chr5:52384559..52387537-chr5:52393582..52396762,3	MCF-7	breast:
4	chr5:52388236..52391143-chr5:52394703..52396954,3	K562	blood:
5	chr5:52395948..52400374-chr5:52403348..52406711,5	MCF-7	breast:
6	chr5:52391585..52394108-chr5:52394132..52397970,3	K562	blood:
7	chr5:52395196..52398086-chr5:52402266..52404408,2	K562	blood:

Variant related genes	Relation type
ENSG00000247796	Chromatin interaction
ENSG00000164172	Chromatin interaction
ENSG00000272123	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10044163	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs10045657	0.86[CHB][hapmap]
rs10072821	0.86[CHB][hapmap]
rs10471372	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs10471831	0.86[CHB][hapmap]
rs10471832	0.86[CHB][hapmap]
rs10940289	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12109479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16880890	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs16880902	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs2052567	0.86[CHB][hapmap]
rs2233213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2233216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2233220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212427	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212428	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212437	1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3212454	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212460	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212462	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212477	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212534	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212538	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212541	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212602	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212608	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212639	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797468	0.86[CHB][hapmap]
rs3797469	0.86[CHB][hapmap]
rs3928414	0.86[EUR][1000 genomes]
rs41308283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7732191	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9292009	0.86[CHB][hapmap]
rs9968622	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9968673	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:52370400-52404600	Weak transcription	Brain Germinal Matrix	brain
3	chr5:52372400-52404400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:52378400-52405000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:52387600-52405000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:52388200-52398400	Strong transcription	HUVEC	blood vessel
7	chr5:52389400-52404800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:52390000-52397600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:52390200-52403800	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr5:52390600-52397200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:52390600-52399600	Strong transcription	NHEK	skin
12	chr5:52390600-52401200	Strong transcription	Dnd41	blood
13	chr5:52390800-52403800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:52391000-52401000	Strong transcription	Duodenum Mucosa	Duodenum
15	chr5:52391000-52403000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr5:52391600-52403200	Weak transcription	Fetal Heart	heart
17	chr5:52392000-52404800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:52392200-52400800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr5:52392200-52401200	Strong transcription	Fetal Muscle Trunk	muscle
20	chr5:52392400-52398600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr5:52392400-52400000	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr5:52392400-52400400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr5:52392400-52401400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr5:52392400-52403000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr5:52392400-52403400	Strong transcription	Liver	Liver
26	chr5:52392400-52404800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr5:52392600-52400400	Strong transcription	Stomach Smooth Muscle	stomach
28	chr5:52392800-52397000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr5:52392800-52397000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr5:52392800-52399400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:52392800-52400200	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr5:52392800-52400400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:52392800-52401000	Strong transcription	Fetal Muscle Leg	muscle
34	chr5:52392800-52401400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:52392800-52403000	Strong transcription	Adipose Nuclei	Adipose
36	chr5:52392800-52403400	Strong transcription	Left Ventricle	heart
37	chr5:52392800-52403600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:52393000-52397400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr5:52393000-52397800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr5:52393000-52405000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr5:52393200-52398000	Strong transcription	NHDF-Ad	bronchial
42	chr5:52393400-52398000	Strong transcription	Fetal Lung	lung
43	chr5:52393400-52399200	Weak transcription	K562	blood
44	chr5:52393800-52404800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr5:52394000-52397400	Strong transcription	Colon Smooth Muscle	Colon
46	chr5:52394000-52398000	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr5:52394000-52400400	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr5:52394200-52400000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr5:52394200-52400200	Strong transcription	Placenta	Placenta
50	chr5:52394200-52401000	Strong transcription	Primary T cells fromperipheralblood	blood

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