Variant report

Variant	rs1139620
Chromosome Location	chr1:153777848-153777849
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153774428..153778178-chr1:153892159..153894443,3	MCF-7	breast:
2	chr1:153775180..153778108-chr1:153780160..153781973,2	MCF-7	breast:
3	chr1:153767398..153773135-chr1:153773279..153780360,13	K562	blood:
4	chr1:153776914..153778870-chr1:153957871..153960450,2	MCF-7	breast:
5	chr1:153748762..153752537-chr1:153776954..153780050,3	K562	blood:
6	chr1:153773297..153774898-chr1:153777098..153779392,2	K562	blood:
7	chr1:153776789..153780334-chr1:153780412..153785020,5	K562	blood:
8	chr1:153777336..153779352-chr1:153950102..153952404,2	MCF-7	breast:
9	chr1:153776385..153778057-chr1:153893375..153895868,2	K562	blood:
10	chr1:153769239..153773675-chr1:153774397..153779052,9	K562	blood:
11	chr1:153755388..153757822-chr1:153776509..153778942,2	K562	blood:
12	chr1:153775358..153778159-chr1:153933970..153936811,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143554	Chromatin interaction
ENSG00000231827	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000143614	Chromatin interaction
ENSG00000143543	Chromatin interaction
ENSG00000272654	Chromatin interaction
ENSG00000143545	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10127484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10494303	0.81[CEU][hapmap]
rs10908525	0.81[AFR][1000 genomes]
rs10908578	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs11264573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap]
rs11264736	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs1127091	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11800001	0.86[ASN][1000 genomes]
rs12117078	1.00[JPT][hapmap]
rs12120118	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124424	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129468	0.93[ASN][1000 genomes]
rs12130611	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133492	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133923	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12142639	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12142733	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12738361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17364880	1.00[JPT][hapmap]
rs2252508	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs35711150	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3791186	0.81[CEU][hapmap]
rs4276953	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4341393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4370789	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4451582	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4540690	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4581307	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4596938	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845360	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs61803655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427300	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427306	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661009	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs6668066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677794	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6690619	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6700115	0.94[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs72694233	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7414227	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7415004	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7522030	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.83[ASN][1000 genomes]
rs7532974	0.88[AFR][1000 genomes]
rs7532982	0.83[AFR][1000 genomes]
rs7554469	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9426935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9426938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427232	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427233	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
4	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	nsv464039	chr1:153708906-153801098	Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv547941	chr1:153708906-153801098	Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv817392	chr1:153724807-153870005	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1139620	GATAD2B	cis	cerebellum	SCAN
rs1139620	HAX1	cis	cerebellum	SCAN
rs1139620	CTAG2	trans	parietal	SCAN
rs1139620	FLG	cis	parietal	SCAN
rs1139620	GBA	cis	parietal	SCAN
rs1139620	SLC27A3	cis	cerebellum	SCAN
rs1139620	DCST2	cis	cerebellum	SCAN
rs1139620	PSMD4	cis	parietal	SCAN
rs1139620	S100A8	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153757000-153779200	Weak transcription	Dnd41	blood
2	chr1:153762600-153779600	Weak transcription	Gastric	stomach
3	chr1:153762600-153779600	Weak transcription	Pancreas	Pancrea
4	chr1:153763600-153780000	Weak transcription	Aorta	Aorta
5	chr1:153763600-153780000	Weak transcription	Ovary	ovary
6	chr1:153763600-153780800	Weak transcription	Colonic Mucosa	Colon
7	chr1:153763800-153779400	Weak transcription	Brain Substantia Nigra	brain
8	chr1:153764000-153779600	Weak transcription	Brain Angular Gyrus	brain
9	chr1:153764400-153778200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:153764400-153779600	Weak transcription	Brain Anterior Caudate	brain
11	chr1:153767000-153779400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:153767600-153782600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:153767800-153779600	Weak transcription	Fetal Lung	lung
14	chr1:153768000-153779600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:153768000-153779600	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:153768000-153781400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:153768200-153779200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:153768200-153779400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:153768200-153779600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:153768200-153779600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:153768400-153779200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:153768400-153779800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:153768800-153779000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:153769800-153778000	Weak transcription	A549	lung
25	chr1:153769800-153779400	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:153769800-153781400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:153770400-153791400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:153770600-153783600	Weak transcription	Fetal Brain Male	brain
29	chr1:153770800-153792400	Strong transcription	Fetal Stomach	stomach
30	chr1:153771200-153779400	Weak transcription	HepG2	liver
31	chr1:153771800-153791800	Strong transcription	Primary T cells from cord blood	blood
32	chr1:153772000-153792000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:153772200-153781200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:153772400-153779600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:153772600-153778000	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr1:153772600-153781400	Weak transcription	Esophagus	oesophagus
37	chr1:153772600-153791600	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr1:153773000-153779400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:153773600-153791800	Strong transcription	Thymus	Thymus
40	chr1:153774000-153801800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:153774200-153778600	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr1:153774600-153778800	Enhancers	Right Ventricle	heart
43	chr1:153774800-153779400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:153775000-153778800	Enhancers	Left Ventricle	heart
45	chr1:153775000-153779000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:153775000-153779800	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr1:153775000-153798800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:153775200-153778400	Genic enhancers	Fetal Muscle Leg	muscle
49	chr1:153775200-153779200	Enhancers	Adipose Nuclei	Adipose
50	chr1:153775400-153778200	Weak transcription	Stomach Smooth Muscle	stomach

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