Variant report

Variant	rs3777162
Chromosome Location	chr5:95293412-95293413
allele	C/T
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	chr5:95293272-95293709	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:95293281-95298477	GM12891	blood:	n/a	n/a
3	UBTF	chr5:95293409-95293426	K562	blood:	n/a	n/a
4	CHD1	chr5:95290276-95298838	IMR90	lung:	n/a	chr5:95296574-95296584
5	MEF2C	chr5:95293358-95293922	GM12878	blood:	n/a	chr5:95293394-95293415 chr5:95293400-95293411 chr5:95293394-95293415 chr5:95293401-95293410
6	POLR2A	chr5:95293315-95296020	HepG2	liver:	n/a	n/a
7	POLR2A	chr5:95293276-95298236	IMR90	lung:	n/a	n/a
8	MEF2A	chr5:95293403-95293965	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:95218170..95220119-chr5:95292473..95294131,2	MCF-7	breast:
2	chr5:95287964..95290450-chr5:95291198..95293883,2	MCF-7	breast:
3	chr5:95204164..95206155-chr5:95291916..95293467,2	K562	blood:
4	chr5:95289886..95294659-chr5:95295662..95298234,5	MCF-7	breast:
5	chr5:95285461..95287509-chr5:95291864..95293445,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251314	TF binding region
ENSG00000118985	Chromatin interaction
ENSG00000251314	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10052503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10069748	0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap]
rs10073752	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10515232	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.94[EUR][1000 genomes]
rs1057963	0.91[CHB][hapmap]
rs1057964	0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap]
rs11741590	0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.82[YRI][hapmap]
rs11744881	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs12055262	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1423268	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs1423269	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs1458017	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs1458018	0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap]
rs17085249	0.91[CHB][hapmap];0.81[CHD][hapmap]
rs17085333	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1841010	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs1862313	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2042340	0.91[CHB][hapmap]
rs2112566	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2161318	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270554	0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap]
rs2348984	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs2546199	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548594	0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.82[YRI][hapmap]
rs3734131	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3756703	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777164	0.84[EUR][1000 genomes]
rs3777165	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777166	1.00[CEU][hapmap];0.91[CHB][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777167	0.84[CEU][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs3777168	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3777171	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777173	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777175	0.84[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777178	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777179	0.88[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777183	0.82[CHB][hapmap]
rs3777184	0.91[CHB][hapmap]
rs3777185	0.91[CHB][hapmap]
rs3777188	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs3777189	0.91[CHB][hapmap]
rs3777190	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs3777193	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs3777194	0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap]
rs3777196	0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap]
rs3777200	0.91[CHB][hapmap];0.84[CHD][hapmap]
rs3777204	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs3777207	0.86[TSI][hapmap]
rs3815768	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs3822750	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4538631	0.82[CHB][hapmap]
rs4563648	0.83[ASN][1000 genomes]
rs4642392	0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap]
rs55841351	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56002885	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57243277	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57595413	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58921760	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59307279	0.92[EUR][1000 genomes]
rs6556894	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861531	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6877821	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881355	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6881872	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6883880	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6885567	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs6889029	0.91[CHB][hapmap]
rs6894651	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6897997	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6898371	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898399	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72656689	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7700895	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7705279	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7705720	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7710422	0.80[EUR][1000 genomes]
rs7716691	0.83[YRI][hapmap]
rs7724599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs889302	0.91[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.85[ASN][1000 genomes]
rs918629	1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes]
rs9314162	0.91[CHB][hapmap]

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	nsv1019566	chr5:95180352-95300677	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2758003	chr5:95231706-95540433	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	esv2759355	chr5:95231706-95540433	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3777162	ERAP1	cis	cerebellum	SCAN
rs3777162	ELL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95260800-95295200	Weak transcription	Primary T cells from cord blood	blood
2	chr5:95262200-95295400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr5:95264800-95293800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr5:95281000-95294000	Weak transcription	Esophagus	oesophagus
5	chr5:95282400-95294000	Weak transcription	Pancreas	Pancrea
6	chr5:95282600-95294000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr5:95284600-95295200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr5:95286000-95293800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr5:95286400-95295200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:95287000-95294800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr5:95288000-95294400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:95289200-95294000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:95290400-95294000	Active TSS	Right Ventricle	heart
14	chr5:95290600-95293600	Enhancers	Brain Substantia Nigra	brain
15	chr5:95290600-95293800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:95290600-95294000	Enhancers	Stomach Mucosa	stomach
17	chr5:95290600-95296800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
18	chr5:95290800-95295000	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr5:95291000-95293800	Enhancers	Brain Angular Gyrus	brain
20	chr5:95291200-95296000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:95291400-95293800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:95291400-95293800	Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr5:95291400-95294000	Enhancers	NHDF-Ad	bronchial
24	chr5:95291400-95296200	Transcr. at gene 5' and 3'	HMEC	breast
25	chr5:95291800-95293800	Weak transcription	Primary B cells from cord blood	blood
26	chr5:95291800-95294200	Enhancers	A549	lung
27	chr5:95292000-95293800	Weak transcription	Left Ventricle	heart
28	chr5:95292000-95293800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr5:95292000-95294000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr5:95292000-95294000	Weak transcription	Ovary	ovary
31	chr5:95292200-95293600	Enhancers	Brain Hippocampus Middle	brain
32	chr5:95292200-95293800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr5:95292200-95293800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr5:95292200-95293800	Active TSS	GM12878-XiMat	blood
35	chr5:95292200-95294000	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr5:95292200-95294000	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr5:95292200-95294000	Active TSS	Psoas Muscle	Psoas
38	chr5:95292200-95294000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr5:95292200-95294000	Active TSS	NHLF	lung
40	chr5:95292200-95294400	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr5:95292200-95294800	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr5:95292400-95293600	Weak transcription	Fetal Intestine Large	intestine
43	chr5:95292400-95293800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:95292400-95293800	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr5:95292400-95294000	Enhancers	Brain Anterior Caudate	brain
46	chr5:95292400-95294000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr5:95292400-95294600	Weak transcription	Fetal Stomach	stomach
48	chr5:95292600-95293600	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr5:95292600-95294000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:95292600-95294600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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