Variant report

Variant	rs4341393
Chromosome Location	chr1:153776666-153776667
allele	C/T
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 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	chr1:153775656..153777183-chr1:153917623..153920101,2	MCF-7	breast:
4	chr1:153767398..153773135-chr1:153773279..153780360,13	K562	blood:
5	chr1:153763846..153765824-chr1:153774129..153777112,2	MCF-7	breast:
6	chr1:153762146..153764067-chr1:153775789..153777743,2	K562	blood:
7	chr1:153776385..153778057-chr1:153893375..153895868,2	K562	blood:
8	chr1:153776152..153777672-chr1:153961984..153964680,2	K562	blood:
9	chr1:153775752..153777404-chr1:153939264..153942069,2	MCF-7	breast:
10	chr1:153769239..153773675-chr1:153774397..153779052,9	K562	blood:
11	chr1:153774458..153777445-chr1:153916897..153919240,3	MCF-7	breast:
12	chr1:153775203..153777547-chr1:153784998..153786855,2	MCF-7	breast:
13	chr1:153755388..153757822-chr1:153776509..153778942,2	K562	blood:
14	chr1:153775358..153778159-chr1:153933970..153936811,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143578	Chromatin interaction
ENSG00000231827	Chromatin interaction
ENSG00000198837	Chromatin interaction
ENSG00000143614	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000177954	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 10 )

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];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs11264573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[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];0.89[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]
rs1139620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800001	0.86[ASN][1000 genomes]
rs12117078	1.00[JPT][hapmap]
rs12120118	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124424	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[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];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133492	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133923	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12142639	0.80[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];0.91[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];0.91[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	0.86[ASN][1000 genomes]
rs3791186	0.81[CEU][hapmap]
rs4276953	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4370789	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4451582	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4596938	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845360	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[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];0.94[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];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs6668066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677794	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[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];0.98[EUR][1000 genomes]
rs72694233	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[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];0.91[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];0.82[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];0.91[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];0.89[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427232	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427233	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4341393	PSMD4	cis	parietal	SCAN
rs4341393	CTAG2	trans	parietal	SCAN
rs4341393	SLC27A3	cis	cerebellum	SCAN
rs4341393	DCST2	cis	cerebellum	SCAN
rs4341393	GBA	cis	parietal	SCAN
rs4341393	S100A8	cis	parietal	SCAN
rs4341393	FLG	cis	parietal	SCAN
rs4341393	GATAD2B	cis	multi-tissue	Pritchard
rs4341393	HAX1	cis	cerebellum	SCAN
rs4341393	GATAD2B	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153757000-153779200	Weak transcription	Dnd41	blood
2	chr1:153762600-153777600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:153762600-153777600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:153762600-153779600	Weak transcription	Gastric	stomach
5	chr1:153762600-153779600	Weak transcription	Pancreas	Pancrea
6	chr1:153763600-153776800	Weak transcription	Right Atrium	heart
7	chr1:153763600-153777800	Weak transcription	Fetal Intestine Large	intestine
8	chr1:153763600-153780000	Weak transcription	Aorta	Aorta
9	chr1:153763600-153780000	Weak transcription	Ovary	ovary
10	chr1:153763600-153780800	Weak transcription	Colonic Mucosa	Colon
11	chr1:153763800-153779400	Weak transcription	Brain Substantia Nigra	brain
12	chr1:153764000-153777000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr1:153764000-153777800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:153764000-153779600	Weak transcription	Brain Angular Gyrus	brain
15	chr1:153764400-153777600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:153764400-153777600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:153764400-153778200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:153764400-153779600	Weak transcription	Brain Anterior Caudate	brain
19	chr1:153764600-153777600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:153764600-153777800	Weak transcription	NHLF	lung
21	chr1:153767000-153779400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:153767600-153782600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:153767800-153779600	Weak transcription	Fetal Lung	lung
24	chr1:153768000-153777600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:153768000-153777800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:153768000-153779600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:153768000-153779600	Weak transcription	Brain Hippocampus Middle	brain
28	chr1:153768000-153781400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:153768200-153777800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:153768200-153779200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:153768200-153779400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:153768200-153779600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr1:153768200-153779600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:153768400-153779200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr1:153768400-153779800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:153768800-153779000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:153769800-153777000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:153769800-153777600	Weak transcription	Hela-S3	cervix
39	chr1:153769800-153777600	Weak transcription	NHEK	skin
40	chr1:153769800-153778000	Weak transcription	A549	lung
41	chr1:153769800-153779400	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:153769800-153781400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr1:153770400-153791400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:153770600-153776800	Strong transcription	Fetal Brain Female	brain
45	chr1:153770600-153783600	Weak transcription	Fetal Brain Male	brain
46	chr1:153770800-153792400	Strong transcription	Fetal Stomach	stomach
47	chr1:153771200-153779400	Weak transcription	HepG2	liver
48	chr1:153771800-153791800	Strong transcription	Primary T cells from cord blood	blood
49	chr1:153772000-153792000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr1:153772200-153781200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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