Variant report

Variant	rs7532400
Chromosome Location	chr1:66998436-66998437
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:66996735-67003737	IMR90	lung:	n/a	n/a
2	SIN3A	chr1:66998414-66999956	H1-hESC	embryonic stem cell:	n/a	n/a
3	CEBPB	chr1:66998429-66998812	IMR90	lung:	n/a	n/a
4	POLR2A	chr1:66997970-67000478	HUVEC	blood vessel:	n/a	n/a
5	MAZ	chr1:66997994-67000458	IMR90	lung:	n/a	chr1:66998876-66998886
6	POLR2A	chr1:66997967-67000176	HUVEC	blood vessel:	n/a	n/a
7	MXI1	chr1:66998034-67001342	IMR90	lung:	n/a	n/a
8	USF1	chr1:66998345-66998675	H1-hESC	embryonic stem cell:	n/a	n/a
9	CHD1	chr1:66997255-67003973	IMR90	lung:	n/a	n/a
10	USF1	chr1:66998345-66998720	H1-hESC	embryonic stem cell:	n/a	n/a
11	REST	chr1:66998238-67000810	H1-neurons	neurons:	n/a	chr1:67000267-67000275 chr1:66999795-66999808 chr1:66999795-66999808 chr1:66999795-66999808 chr1:67000301-67000311

Variant related genes	Relation type
SGIP1	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10493408	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11208896	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11208898	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11208900	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11208901	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11208902	1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs12022565	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12025668	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12040232	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12043594	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12046904	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12048885	0.93[CEU][hapmap];0.90[CHB][hapmap];0.91[YRI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12567898	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1338196	0.93[ASN][1000 genomes]
rs1338199	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1338201	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1338202	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1338203	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1338206	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1338207	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1445578	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1445579	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17129039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17129041	0.84[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17129043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17129062	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17129064	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17129065	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4655614	0.94[ASN][1000 genomes]
rs4655616	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs57941297	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6664942	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6665299	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6689119	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6689313	0.82[ASW][hapmap];0.86[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6693644	0.94[ASN][1000 genomes]
rs6697068	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6699123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72916320	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72934129	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72934131	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72934142	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72934143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72934153	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7532598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7532613	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7533806	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7533837	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7544247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544505	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7549881	0.94[ASN][1000 genomes]
rs967324	1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7532400	DIRAS3	cis	cerebellum	SCAN
rs7532400	SGIP1	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:66991800-66998600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:66997600-66998600	Enhancers	Fetal Heart	heart
3	chr1:66997800-66998600	Enhancers	Fetal Brain Male	brain
4	chr1:66998000-66998600	Enhancers	Fetal Kidney	kidney
5	chr1:66998000-66999000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:66998200-66998600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:66998200-66998600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:66998200-66998600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
9	chr1:66998200-66998800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:66998200-66998800	Flanking Active TSS	Primary T cells from cord blood	blood
11	chr1:66998200-66998800	Flanking Active TSS	Brain Hippocampus Middle	brain
12	chr1:66998200-66998800	Flanking Active TSS	NHDF-Ad	bronchial
13	chr1:66998200-66998800	Flanking Active TSS	NHLF	lung
14	chr1:66998200-66998800	Flanking Active TSS	Osteobl	bone
15	chr1:66998200-66999000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:66998200-66999000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr1:66998200-66999000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:66998200-66999000	Flanking Active TSS	Brain Germinal Matrix	brain
19	chr1:66998200-66999200	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
20	chr1:66998200-66999200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
21	chr1:66998200-66999400	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr1:66998200-67000200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
23	chr1:66998200-67000200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr1:66998200-67000400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:66998200-67000400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:66998200-67000400	Flanking Active TSS	HUVEC	blood vessel
27	chr1:66998200-67001000	Active TSS	Fetal Brain Female	brain
28	chr1:66998400-66998600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr1:66998400-66998600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:66998400-66998600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
31	chr1:66998400-66998600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
32	chr1:66998400-66998600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr1:66998400-66998600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
34	chr1:66998400-66998600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
35	chr1:66998400-66998600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr1:66998400-66998600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr1:66998400-66998600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:66998400-66998600	Bivalent Enhancer	Adipose Nuclei	Adipose
39	chr1:66998400-66998600	Bivalent Enhancer	Colon Smooth Muscle	Colon
40	chr1:66998400-66998600	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr1:66998400-66998600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
42	chr1:66998400-66998600	Enhancers	Fetal Lung	lung
43	chr1:66998400-66998600	Bivalent Enhancer	Fetal Muscle Leg	muscle
44	chr1:66998400-66998600	Enhancers	Lung	lung
45	chr1:66998400-66998600	Enhancers	Pancreas	Pancrea
46	chr1:66998400-66998600	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas
47	chr1:66998400-66998600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
48	chr1:66998400-66998600	Enhancers	Right Atrium	heart
49	chr1:66998400-66998600	Enhancers	Right Ventricle	heart
50	chr1:66998400-66998600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle

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