Variant report

Variant	rs4532127
Chromosome Location	chr3:52727736-52727737
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52727265..52729020-chr3:52730651..52732360,2	MCF-7	breast:
2	chr3:52720704..52722447-chr3:52727670..52729403,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000016864	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10510759	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11510435	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12107484	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17052357	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17052404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1963813	0.97[AFR][1000 genomes]
rs34173244	1.00[EUR][1000 genomes]
rs4687685	1.00[MEX][hapmap]
rs56134416	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56156188	1.00[EUR][1000 genomes]
rs56276589	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56665533	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57008939	1.00[EUR][1000 genomes]
rs57298447	1.00[EUR][1000 genomes]
rs57757646	1.00[EUR][1000 genomes]
rs57789542	1.00[EUR][1000 genomes]
rs57869735	1.00[EUR][1000 genomes]
rs57946083	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58409398	1.00[EUR][1000 genomes]
rs58528592	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58564212	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59638016	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59869286	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60040519	1.00[EUR][1000 genomes]
rs60058353	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60256157	1.00[EUR][1000 genomes]
rs60311166	1.00[EUR][1000 genomes]
rs60770874	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60830326	1.00[EUR][1000 genomes]
rs61220667	1.00[EUR][1000 genomes]
rs61538294	1.00[EUR][1000 genomes]
rs6445536	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6762788	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6769720	1.00[EUR][1000 genomes]
rs6774097	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6780005	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6780397	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6803492	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs72947584	0.81[AFR][1000 genomes]
rs72950424	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72950432	1.00[EUR][1000 genomes]
rs72950437	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960237	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960240	1.00[EUR][1000 genomes]
rs72960260	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960274	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960281	1.00[EUR][1000 genomes]
rs72960285	1.00[EUR][1000 genomes]
rs72965177	1.00[EUR][1000 genomes]
rs72965181	1.00[EUR][1000 genomes]
rs73839126	1.00[EUR][1000 genomes]
rs73839129	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7643568	1.00[ASW][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs7645785	1.00[EUR][1000 genomes]
rs764636	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7647992	1.00[EUR][1000 genomes]
rs934839	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4532127	SPCS1	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52721000-52728000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:52721000-52730400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:52721000-52734400	Strong transcription	Fetal Stomach	stomach
4	chr3:52721000-52738600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:52721200-52730600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:52721200-52731600	Strong transcription	H9 Cell Line	embryonic stem cell
7	chr3:52721200-52732200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:52721200-52732200	Strong transcription	Fetal Muscle Trunk	muscle
9	chr3:52721200-52732200	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:52721200-52733000	Strong transcription	Stomach Smooth Muscle	stomach
11	chr3:52721200-52734400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr3:52721400-52730800	Strong transcription	Lung	lung
13	chr3:52721400-52731800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:52721400-52732000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:52721400-52732200	Strong transcription	Brain Angular Gyrus	brain
16	chr3:52721400-52732200	Strong transcription	Colon Smooth Muscle	Colon
17	chr3:52721400-52732400	Strong transcription	Brain Anterior Caudate	brain
18	chr3:52721400-52732400	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:52721400-52732800	Strong transcription	Fetal Brain Female	brain
20	chr3:52721400-52732800	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:52721400-52733000	Strong transcription	Adipose Nuclei	Adipose
22	chr3:52721400-52734000	Strong transcription	Primary B cells from cord blood	blood
23	chr3:52721400-52734200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:52721400-52734400	Strong transcription	Brain Hippocampus Middle	brain
25	chr3:52721400-52734400	Strong transcription	Fetal Lung	lung
26	chr3:52721400-52734400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr3:52721400-52734600	Strong transcription	Primary T cells from cord blood	blood
28	chr3:52721400-52735800	Strong transcription	Fetal Muscle Leg	muscle
29	chr3:52721600-52730400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:52721600-52730400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:52721600-52730800	Strong transcription	Spleen	Spleen
32	chr3:52721600-52731200	Strong transcription	HSMMtube	muscle
33	chr3:52721600-52732000	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr3:52721600-52732000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:52721600-52732000	Strong transcription	Brain Cingulate Gyrus	brain
36	chr3:52721600-52732000	Strong transcription	Left Ventricle	heart
37	chr3:52721600-52732000	Strong transcription	Ovary	ovary
38	chr3:52721600-52732000	Strong transcription	Right Ventricle	heart
39	chr3:52721600-52732200	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:52721600-52732400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:52721600-52732400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:52721600-52733600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:52721600-52734200	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr3:52721600-52734200	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:52721600-52734400	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr3:52721600-52734400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:52721600-52734400	Strong transcription	Thymus	Thymus
48	chr3:52721800-52729400	Strong transcription	Small Intestine	intestine
49	chr3:52721800-52731200	Strong transcription	Primary B cells from peripheral blood	blood
50	chr3:52721800-52731200	Strong transcription	Primary T cells fromperipheralblood	blood

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