Variant report

Variant	rs1373109
Chromosome Location	chr4:16214954-16214955
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:16209849..16215808-chr4:16226595..16229936,7	MCF-7	breast:
2	chr4:16212529..16219737-chr4:16225844..16229602,8	MCF-7	breast:
3	chr4:16205687..16210095-chr4:16211514..16215415,4	K562	blood:
4	chr4:16212101..16215841-chr4:16226688..16231114,5	K562	blood:
5	chr4:16213214..16216193-chr4:16226396..16228188,2	K562	blood:

Variant related genes	Relation type
ENSG00000263327	Chromatin interaction
ENSG00000169762	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10007592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10017532	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs10516296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11946259	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1443368	0.96[EUR][1000 genomes]
rs1443369	0.96[EUR][1000 genomes]
rs1443370	1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes]
rs1621739	0.83[AFR][1000 genomes]
rs16893164	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1712479	0.89[EUR][1000 genomes]
rs17479949	1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs2011754	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028631	0.84[AFR][1000 genomes]
rs28377010	0.92[EUR][1000 genomes]
rs28403341	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28427433	0.82[AFR][1000 genomes]
rs28481627	0.95[ASN][1000 genomes]
rs28485928	0.94[EUR][1000 genomes]
rs28496446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28517428	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs28537328	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs28654954	0.82[AFR][1000 genomes]
rs28726676	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28757814	0.90[ASN][1000 genomes]
rs317852	0.81[AFR][1000 genomes]
rs317858	0.90[EUR][1000 genomes]
rs317864	0.81[AFR][1000 genomes]
rs35046072	0.94[EUR][1000 genomes]
rs35367114	0.84[EUR][1000 genomes]
rs35931597	0.86[AFR][1000 genomes]
rs4235382	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs4501221	0.81[AFR][1000 genomes]
rs57110573	0.95[ASN][1000 genomes]
rs58468710	0.95[ASN][1000 genomes]
rs6823623	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7359	1.00[JPT][hapmap]
rs73798865	0.95[ASN][1000 genomes]
rs73798866	0.95[ASN][1000 genomes]
rs73798869	0.95[ASN][1000 genomes]
rs73798871	0.86[ASN][1000 genomes]
rs73798874	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73798875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73798883	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73802012	0.81[ASN][1000 genomes]
rs7664407	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7668729	1.00[JPT][hapmap]
rs7690701	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs961450	0.96[EUR][1000 genomes]
rs975229	0.86[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs9946	1.00[JPT][hapmap]
rs9995025	0.86[AFR][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	nsv998299	chr4:16031459-16226466	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16181200-16223800	Weak transcription	Fetal Brain Male	brain
2	chr4:16193000-16216000	Weak transcription	Spleen	Spleen
3	chr4:16193000-16225800	Weak transcription	Colonic Mucosa	Colon
4	chr4:16193200-16225800	Weak transcription	Fetal Brain Female	brain
5	chr4:16198600-16216400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:16198600-16221200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:16198600-16222400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:16198800-16218800	Weak transcription	HSMM	muscle
9	chr4:16198800-16225600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:16198800-16226000	Weak transcription	NHEK	skin
11	chr4:16198800-16226400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:16199800-16215800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:16200800-16218000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr4:16202800-16220800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr4:16204800-16226600	Weak transcription	NH-A	brain
16	chr4:16205200-16225600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:16206400-16216000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:16206400-16218400	Weak transcription	Fetal Lung	lung
19	chr4:16206600-16218400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr4:16207400-16216000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr4:16207400-16223600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:16208400-16219000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr4:16208400-16224400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr4:16208400-16225200	Weak transcription	Fetal Kidney	kidney
25	chr4:16208400-16225800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:16208800-16216000	Weak transcription	Psoas Muscle	Psoas
27	chr4:16208800-16216600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:16208800-16225600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr4:16208800-16225600	Weak transcription	Esophagus	oesophagus
30	chr4:16208800-16225600	Weak transcription	Gastric	stomach
31	chr4:16208800-16225800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:16208800-16225800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr4:16208800-16227200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr4:16209000-16217000	Weak transcription	HMEC	breast
35	chr4:16209000-16225600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr4:16209200-16216600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr4:16209200-16223400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr4:16209200-16225600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:16209200-16225600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr4:16209400-16226200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:16209400-16226200	Weak transcription	HSMMtube	muscle
42	chr4:16209600-16215800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr4:16209600-16221400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr4:16210400-16225800	Weak transcription	Brain Germinal Matrix	brain
45	chr4:16211200-16215000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:16211200-16215600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr4:16211200-16215800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr4:16212000-16217800	Weak transcription	Aorta	Aorta
49	chr4:16212000-16220600	Weak transcription	A549	lung
50	chr4:16212200-16216000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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