Variant report

Variant	rs1127091
Chromosome Location	chr1:153779412-153779413
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153777962..153780405-chr1:153929432..153931611,2	K562	blood:
2	chr1:153767398..153773135-chr1:153773279..153780360,13	K562	blood:
3	chr1:153748762..153752537-chr1:153776954..153780050,3	K562	blood:
4	chr1:153778414..153782533-chr1:153962253..153965018,3	K562	blood:
5	chr1:153774020..153776363-chr1:153779136..153780973,3	K562	blood:
6	chr1:153779392..153782114-chr1:153944951..153947637,3	K562	blood:
7	chr1:153778310..153780688-chr1:153963201..153964782,2	MCF-7	breast:
8	chr1:153776789..153780334-chr1:153780412..153785020,5	K562	blood:
9	chr1:153779066..153784050-chr1:153787162..153790475,4	K562	blood:
10	chr1:153779392..153782114-chr1:153946020..153947637,2	K562	blood:
11	chr1:153777991..153779497-chr1:153782231..153784183,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000177954	Chromatin interaction
ENSG00000231827	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000160741	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10127484	1.00[CEU][hapmap]
rs10494303	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs10908578	0.89[GIH][hapmap];0.87[TSI][hapmap]
rs11264573	1.00[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap]
rs11264736	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs1139620	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs12120118	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12124424	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12130611	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12133492	0.87[EUR][1000 genomes]
rs12133923	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142639	0.80[EUR][1000 genomes]
rs12142733	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs12738361	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2252508	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs3791186	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs4276953	0.83[EUR][1000 genomes]
rs4341393	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs4370789	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4451582	0.96[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs4540690	0.87[EUR][1000 genomes]
rs4581307	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4596938	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4845360	0.87[GIH][hapmap]
rs61803655	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6427300	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6427306	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6661009	0.96[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap]
rs6664419	0.80[AMR][1000 genomes]
rs6668066	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs6677794	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6690619	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6700115	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72694233	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7414227	0.90[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7415004	0.85[AFR][1000 genomes]
rs7522030	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap]
rs7532974	0.87[AFR][1000 genomes]
rs7532982	0.81[AFR][1000 genomes]
rs7554469	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9426935	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9426938	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9427220	0.80[AMR][1000 genomes]
rs9427232	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9427233	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
9	esv1830663	chr1:153779296-153807816	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	esv1825546	chr1:153779296-153821716	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	esv1825076	chr1:153779296-153843413	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1127091	S100A8	cis	parietal	SCAN
rs1127091	HAX1	cis	cerebellum	SCAN
rs1127091	GBA	cis	parietal	SCAN
rs1127091	FLG	cis	parietal	SCAN
rs1127091	DCST2	cis	cerebellum	SCAN
rs1127091	CTAG2	trans	parietal	SCAN
rs1127091	GATAD2B	cis	cerebellum	SCAN
rs1127091	CREB3L4	cis	multi-tissue	Pritchard
rs1127091	SLC27A3	cis	cerebellum	SCAN
rs1127091	PSMD4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153762600-153779600	Weak transcription	Gastric	stomach
2	chr1:153762600-153779600	Weak transcription	Pancreas	Pancrea
3	chr1:153763600-153780000	Weak transcription	Aorta	Aorta
4	chr1:153763600-153780000	Weak transcription	Ovary	ovary
5	chr1:153763600-153780800	Weak transcription	Colonic Mucosa	Colon
6	chr1:153764000-153779600	Weak transcription	Brain Angular Gyrus	brain
7	chr1:153764400-153779600	Weak transcription	Brain Anterior Caudate	brain
8	chr1:153767600-153782600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:153767800-153779600	Weak transcription	Fetal Lung	lung
10	chr1:153768000-153779600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:153768000-153779600	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:153768000-153781400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:153768200-153779600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:153768200-153779600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:153768400-153779800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:153769800-153781400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:153770400-153791400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:153770600-153783600	Weak transcription	Fetal Brain Male	brain
19	chr1:153770800-153792400	Strong transcription	Fetal Stomach	stomach
20	chr1:153771800-153791800	Strong transcription	Primary T cells from cord blood	blood
21	chr1:153772000-153792000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:153772200-153781200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:153772400-153779600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:153772600-153781400	Weak transcription	Esophagus	oesophagus
25	chr1:153772600-153791600	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:153773600-153791800	Strong transcription	Thymus	Thymus
27	chr1:153774000-153801800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:153775000-153779800	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr1:153775000-153798800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:153775600-153779600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:153775600-153779600	Weak transcription	Fetal Kidney	kidney
32	chr1:153775800-153779600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr1:153776400-153787800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr1:153776400-153791600	Strong transcription	Fetal Muscle Trunk	muscle
35	chr1:153776800-153779600	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr1:153777000-153779600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:153777000-153780000	Weak transcription	Spleen	Spleen
38	chr1:153777200-153782400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:153777400-153801000	Strong transcription	Fetal Intestine Small	intestine
40	chr1:153777600-153779600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:153777600-153779600	Genic enhancers	Hela-S3	cervix
42	chr1:153777600-153785800	Strong transcription	Brain Germinal Matrix	brain
43	chr1:153777600-153791200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:153777800-153779600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:153777800-153791600	Strong transcription	Liver	Liver
46	chr1:153777800-153792000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:153777800-153792200	Strong transcription	Fetal Intestine Large	intestine
48	chr1:153777800-153792400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:153777800-153792800	Strong transcription	Placenta	Placenta
50	chr1:153777800-153793200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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