Variant report

Variant	rs4363451
Chromosome Location	chr1:153790501-153790502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153783970..153785844-chr1:153789077..153791186,2	K562	blood:
2	chr1:153780797..153783971-chr1:153788567..153790595,3	MCF-7	breast:
3	chr1:153788802..153791182-chr1:153963012..153964796,2	K562	blood:
4	chr1:153788125..153790584-chr1:153792328..153794011,2	MCF-7	breast:
5	chr1:153790058..153791685-chr1:153891710..153895601,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143614	Chromatin interaction
ENSG00000177954	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10127983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs10559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs10752613	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10796956	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs10908558	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1110165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs11264532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap]
rs11264619	0.84[AFR][1000 genomes]
rs11264680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs11264743	1.00[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs11264866	0.82[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap]
rs11581644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11583152	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11583896	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11585416	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11587151	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11589857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11590099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12022158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12022730	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12027783	0.80[AFR][1000 genomes]
rs12028398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12032914	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs12033835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs12038577	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12041850	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12041920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12042562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12042989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12043350	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs12401565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap]
rs12403956	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs12564669	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12567313	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1572788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs34805562	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3748848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs3791187	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4077168	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4391701	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4508047	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4520447	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4595397	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4612664	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap]
rs4845576	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845578	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4845583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs58095661	0.84[AFR][1000 genomes]
rs59308681	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59340135	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59678326	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6666703	0.80[AFR][1000 genomes]
rs6672856	0.93[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs6680140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs6694061	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6700451	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6701341	0.82[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap]
rs72694220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72694231	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72694234	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7512766	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7552274	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs946682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs9660089	0.84[EUR][1000 genomes];0.87[ASN][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
rs4363451	GATAD2B	cis	cerebellum	SCAN
rs4363451	SLC39A1	cis	cerebellum	SCAN
rs4363451	PKLR	cis	parietal	SCAN
rs4363451	RAB13	cis	lymphoblastoid	seeQTL
rs4363451	SPRR2D	cis	parietal	SCAN
rs4363451	LASS2	cis	parietal	SCAN
rs4363451	CRTC2	cis	lymphoblastoid	seeQTL
rs4363451	FLG	cis	parietal	SCAN
rs4363451	HAX1	cis	parietal	SCAN
rs4363451	SLC27A3	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153770400-153791400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:153770800-153792400	Strong transcription	Fetal Stomach	stomach
3	chr1:153771800-153791800	Strong transcription	Primary T cells from cord blood	blood
4	chr1:153772000-153792000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:153772600-153791600	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:153773600-153791800	Strong transcription	Thymus	Thymus
7	chr1:153774000-153801800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:153775000-153798800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:153776400-153791600	Strong transcription	Fetal Muscle Trunk	muscle
10	chr1:153777400-153801000	Strong transcription	Fetal Intestine Small	intestine
11	chr1:153777600-153791200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:153777800-153791600	Strong transcription	Liver	Liver
13	chr1:153777800-153792000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:153777800-153792200	Strong transcription	Fetal Intestine Large	intestine
15	chr1:153777800-153792400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:153777800-153792800	Strong transcription	Placenta	Placenta
17	chr1:153777800-153793200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:153777800-153793800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:153778200-153791800	Strong transcription	Fetal Brain Female	brain
20	chr1:153778200-153791800	Strong transcription	Stomach Smooth Muscle	stomach
21	chr1:153778400-153791600	Strong transcription	Fetal Muscle Leg	muscle
22	chr1:153778400-153820400	Weak transcription	Stomach Mucosa	stomach
23	chr1:153778600-153791600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:153779000-153792200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:153779200-153792200	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr1:153779200-153792200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:153779200-153793400	Strong transcription	Fetal Thymus	thymus
28	chr1:153779200-153794200	Strong transcription	Dnd41	blood
29	chr1:153779400-153791200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:153779400-153791600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:153779400-153791600	Strong transcription	NH-A	brain
32	chr1:153779400-153792000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:153779400-153792000	Strong transcription	Primary B cells from peripheral blood	blood
34	chr1:153779400-153792000	Strong transcription	Duodenum Mucosa	Duodenum
35	chr1:153779400-153792200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:153779400-153792200	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr1:153779400-153792200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:153779400-153792200	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr1:153779400-153792200	Strong transcription	Osteobl	bone
40	chr1:153779400-153792600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:153779400-153792800	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:153779400-153793800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:153779600-153791400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:153779600-153791600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:153779600-153791600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:153779600-153791600	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:153779600-153791600	Strong transcription	Lung	lung
48	chr1:153779600-153791600	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr1:153779600-153791600	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:153779600-153791800	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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