Variant report

Variant	rs3776176
Chromosome Location	chr5:100232575-100232576
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:100231184..100232741-chr5:100236415..100237958,2	MCF-7	breast:

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10043056	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10044903	0.82[EUR][1000 genomes]
rs10052474	0.82[EUR][1000 genomes]
rs10058901	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10059470	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10059846	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10069305	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10078934	0.83[EUR][1000 genomes]
rs10214216	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10463771	0.83[EUR][1000 genomes]
rs10463772	0.83[EUR][1000 genomes]
rs10477661	0.89[EUR][1000 genomes]
rs10478633	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10478649	0.89[EUR][1000 genomes]
rs11241752	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs11241755	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs11584	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11738152	0.83[EUR][1000 genomes]
rs11742480	0.83[EUR][1000 genomes]
rs11742504	0.83[EUR][1000 genomes]
rs12153670	0.83[EUR][1000 genomes]
rs13355889	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13358325	0.83[EUR][1000 genomes]
rs1423380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423384	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423385	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1428439	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1541676	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs1559058	0.83[EUR][1000 genomes]
rs1559059	0.82[EUR][1000 genomes]
rs17723545	0.83[EUR][1000 genomes]
rs17724185	0.82[EUR][1000 genomes]
rs17725452	0.84[EUR][1000 genomes]
rs17725678	0.83[EUR][1000 genomes]
rs17726244	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17780091	0.81[EUR][1000 genomes]
rs17780273	0.81[EUR][1000 genomes]
rs17780471	0.81[EUR][1000 genomes]
rs17780525	0.83[EUR][1000 genomes]
rs17782041	0.83[EUR][1000 genomes]
rs17782250	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1820150	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1833862	0.83[EUR][1000 genomes]
rs2059845	0.82[EUR][1000 genomes]
rs2059846	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2400313	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2544913	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2544920	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs2548256	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2548257	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2548263	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2548276	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2548278	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2548279	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2548280	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2725116	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2725124	0.83[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28413976	0.81[EUR][1000 genomes]
rs3756350	0.82[EUR][1000 genomes]
rs3756351	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3756352	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3756353	0.81[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3756354	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3756355	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776167	0.83[EUR][1000 genomes]
rs3776168	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3776170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3776171	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776174	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3822366	0.82[EUR][1000 genomes]
rs3846627	0.82[EUR][1000 genomes]
rs3857365	0.82[EUR][1000 genomes]
rs3909452	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4702991	0.82[EUR][1000 genomes]
rs4703126	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs4703127	0.83[EUR][1000 genomes]
rs4703128	0.81[EUR][1000 genomes]
rs4703130	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4703131	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs4703133	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55849330	0.80[EUR][1000 genomes]
rs55959219	0.83[EUR][1000 genomes]
rs59030588	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59490571	0.83[EUR][1000 genomes]
rs60663279	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60853907	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs726971	0.81[EUR][1000 genomes]
rs72778607	0.82[EUR][1000 genomes]
rs72778613	0.81[EUR][1000 genomes]
rs72778620	0.81[EUR][1000 genomes]
rs72778635	0.85[EUR][1000 genomes]
rs7447673	0.83[EUR][1000 genomes]
rs7703643	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7737721	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9327319	0.83[EUR][1000 genomes]
rs9327323	0.83[EUR][1000 genomes]
rs9327327	0.83[EUR][1000 genomes]
rs966257	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023765	chr5:99915011-100733755	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	esv1834675	chr5:100143084-100535029	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3776176	ST8SIA4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100200200-100234400	Weak transcription	Fetal Brain Male	brain
2	chr5:100208000-100235800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:100219000-100233400	Weak transcription	Brain Germinal Matrix	brain
4	chr5:100225200-100233800	Weak transcription	Thymus	Thymus
5	chr5:100226400-100233800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr5:100226400-100235600	Weak transcription	Placenta	Placenta
7	chr5:100226800-100233800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:100227000-100234400	Weak transcription	Right Atrium	heart
9	chr5:100227000-100235600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:100227200-100232800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:100227200-100232800	Weak transcription	Osteobl	bone
12	chr5:100227200-100235600	Weak transcription	Fetal Lung	lung
13	chr5:100228000-100232600	Strong transcription	Primary B cells from peripheral blood	blood
14	chr5:100229200-100235400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:100230200-100235200	Enhancers	Primary T cells from cord blood	blood
16	chr5:100230400-100233800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr5:100230800-100236400	Transcr. at gene 5' and 3'	Dnd41	blood
18	chr5:100231000-100233800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr5:100231000-100235400	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr5:100231000-100235400	Weak transcription	HUVEC	blood vessel
21	chr5:100231200-100232600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:100231200-100232600	ZNF genes & repeats	GM12878-XiMat	blood
23	chr5:100231200-100235400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:100231200-100235600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr5:100231400-100232600	Genic enhancers	Primary B cells from cord blood	blood
26	chr5:100231400-100233000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr5:100231400-100234400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr5:100231600-100232600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr5:100231600-100232600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr5:100231600-100232800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:100231600-100232800	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr5:100231800-100233800	Genic enhancers	Primary monocytes fromperipheralblood	blood
33	chr5:100231800-100233800	Genic enhancers	Monocytes-CD14+_RO01746	blood
34	chr5:100232000-100235600	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr5:100232200-100234400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr5:100232200-100235400	Weak transcription	Fetal Thymus	thymus
37	chr5:100232400-100232600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr5:100232400-100232800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr5:100232400-100233800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr5:100232400-100235000	Enhancers	Primary hematopoietic stem cells	blood
41	chr5:100232400-100235600	Enhancers	Primary T helper cells fromperipheralblood	blood

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