Variant report

Variant	rs2548278
Chromosome Location	chr5:100165117-100165118
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	chr5:100163874..100166036-chr5:100222843..100225362,2	MCF-7	breast:

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10043056	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10044903	0.84[EUR][1000 genomes]
rs10052474	0.84[EUR][1000 genomes]
rs10058901	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10059470	0.90[EUR][1000 genomes]
rs10059846	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10069305	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10075853	0.86[GIH][hapmap];0.83[TSI][hapmap]
rs10078934	0.85[EUR][1000 genomes]
rs10214216	0.91[EUR][1000 genomes]
rs10463771	0.85[EUR][1000 genomes]
rs10463772	0.85[EUR][1000 genomes]
rs10477661	0.85[EUR][1000 genomes]
rs10478599	0.86[GIH][hapmap];0.83[TSI][hapmap]
rs10478633	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10478649	0.85[EUR][1000 genomes]
rs11241752	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs11241755	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs11584	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11738152	0.85[EUR][1000 genomes]
rs11742480	0.84[EUR][1000 genomes]
rs11742504	0.84[EUR][1000 genomes]
rs12153670	0.92[GIH][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs13355889	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13358325	0.92[GIH][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs1423380	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1423384	1.00[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1423385	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1428439	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1541676	0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs1559058	0.85[EUR][1000 genomes]
rs1559059	0.85[EUR][1000 genomes]
rs17723545	0.85[EUR][1000 genomes]
rs17724185	0.85[EUR][1000 genomes]
rs17725452	0.81[EUR][1000 genomes]
rs17725678	0.81[EUR][1000 genomes]
rs17726244	0.86[EUR][1000 genomes]
rs17780091	0.84[EUR][1000 genomes]
rs17780273	0.84[EUR][1000 genomes]
rs17780471	0.84[EUR][1000 genomes]
rs17780525	0.85[EUR][1000 genomes]
rs17782041	0.81[EUR][1000 genomes]
rs17782250	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs1820150	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1833862	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs2059845	0.83[EUR][1000 genomes]
rs2059846	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2400313	1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2544913	1.00[CEU][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2544920	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2548256	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2548257	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548263	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2548276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2548279	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2548280	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2725116	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2725124	0.87[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28413976	0.84[EUR][1000 genomes]
rs3756350	0.85[EUR][1000 genomes]
rs3756351	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3756352	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3756353	0.94[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3756354	1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3756355	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3776167	0.92[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs3776168	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776170	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776171	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3776174	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3776176	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]
rs3822366	0.85[EUR][1000 genomes]
rs3846627	0.83[EUR][1000 genomes]
rs3857365	0.83[EUR][1000 genomes]
rs3909452	0.83[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4702991	0.84[EUR][1000 genomes]
rs4703126	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs4703127	0.85[EUR][1000 genomes]
rs4703128	0.82[EUR][1000 genomes]
rs4703130	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4703131	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs4703133	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55849330	0.83[EUR][1000 genomes]
rs55959219	0.81[EUR][1000 genomes]
rs59030588	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59490571	0.82[EUR][1000 genomes]
rs60663279	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60853907	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs726971	0.84[EUR][1000 genomes]
rs72778607	0.85[EUR][1000 genomes]
rs72778613	0.84[EUR][1000 genomes]
rs72778620	0.84[EUR][1000 genomes]
rs72778635	0.82[EUR][1000 genomes]
rs7447673	0.85[EUR][1000 genomes]
rs7703643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7737721	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9327319	0.85[EUR][1000 genomes]
rs9327323	0.85[EUR][1000 genomes]
rs9327327	0.85[EUR][1000 genomes]
rs966257	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021183	chr5:99625857-100221426	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	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
3	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2548278	FLJ37035	trans	cerebellum	SCAN
rs2548278	ST8SIA4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100147600-100218000	Weak transcription	Thymus	Thymus
2	chr5:100147800-100179000	Weak transcription	Fetal Thymus	thymus
3	chr5:100148600-100173200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr5:100159800-100170800	Strong transcription	Dnd41	blood
5	chr5:100161800-100165200	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr5:100162000-100165200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr5:100164000-100165800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:100164000-100173800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr5:100164200-100171800	Weak transcription	Fetal Stomach	stomach
10	chr5:100164200-100174800	Weak transcription	Placenta	Placenta
11	chr5:100164200-100176200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr5:100164400-100170200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:100164400-100173600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr5:100164400-100175000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr5:100164400-100175800	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr5:100164600-100168400	Weak transcription	Primary B cells from cord blood	blood
17	chr5:100164600-100174800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr5:100164600-100175000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr5:100164800-100165200	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr5:100164800-100168000	Weak transcription	Small Intestine	intestine
21	chr5:100164800-100169400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr5:100164800-100170200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr5:100164800-100170400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:100165000-100165400	Enhancers	GM12878-XiMat	blood
25	chr5:100165000-100165600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:100165000-100165800	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr5:100165000-100166600	Weak transcription	Left Ventricle	heart
28	chr5:100165000-100167200	Weak transcription	Brain Substantia Nigra	brain
29	chr5:100165000-100168200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr5:100165000-100168200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:100165000-100168400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr5:100165000-100168400	Weak transcription	NHEK	skin
33	chr5:100165000-100168600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr5:100165000-100168600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:100165000-100173600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr5:100165000-100173600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr5:100165000-100174800	Weak transcription	Primary T cells from cord blood	blood
38	chr5:100165000-100175800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:100165000-100176200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr5:100165000-100176800	Weak transcription	Primary T cells fromperipheralblood	blood

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