Variant report

Variant	rs4315786
Chromosome Location	chr4:6969727-6969728
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:6962320..6964054-chr4:6967764..6970067,3	K562	blood:
2	chr4:6969313..6971458-chr4:6985802..6989389,3	K562	blood:
3	chr4:6968058..6971311-chr4:6972075..6975359,5	K562	blood:
4	chr4:6918816..6920459-chr4:6968873..6971872,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132405	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10009332	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10013211	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10013696	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10015163	0.81[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10019256	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10019900	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10022657	0.92[CEU][hapmap]
rs10022869	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10032908	0.92[CEU][hapmap]
rs10155208	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10804990	0.95[JPT][hapmap]
rs10937762	0.84[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap]
rs10937763	0.95[JPT][hapmap]
rs10937766	0.83[ASN][1000 genomes]
rs10937768	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs10937769	0.90[ASN][1000 genomes]
rs10937771	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11723686	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11728984	1.00[JPT][hapmap]
rs11731681	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11732389	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs11732887	0.82[ASN][1000 genomes]
rs11733522	0.84[ASN][1000 genomes]
rs12119	0.81[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.80[TSI][hapmap]
rs12512922	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12646620	0.84[ASN][1000 genomes]
rs12646621	0.84[ASN][1000 genomes]
rs12648134	0.81[CEU][hapmap];0.81[CHB][hapmap];0.83[GIH][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12650200	0.92[CEU][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12650264	0.92[CEU][hapmap];0.91[GIH][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13103361	0.84[ASN][1000 genomes]
rs13140943	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13435015	0.85[JPT][hapmap]
rs17742611	0.92[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17743234	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2301820	0.89[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2301821	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28380685	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28392702	0.89[ASN][1000 genomes]
rs28463777	0.84[ASN][1000 genomes]
rs28523495	0.84[ASN][1000 genomes]
rs28703753	0.81[ASN][1000 genomes]
rs34173965	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35296019	0.83[ASN][1000 genomes]
rs35490604	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35772786	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3857168	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3857169	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3857170	0.92[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3892145	0.81[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3892976	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41516949	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs4234790	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4290891	0.82[ASN][1000 genomes]
rs4346651	0.85[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs4432749	0.90[JPT][hapmap]
rs4484301	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4608812	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4689558	0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs4689562	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4689571	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4689572	0.92[CEU][hapmap];0.88[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56307635	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58935653	0.84[ASN][1000 genomes]
rs6446552	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs6446553	0.80[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6831368	0.85[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs6831590	0.81[ASN][1000 genomes]
rs6834007	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6848114	0.85[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6852468	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7664348	0.84[ASN][1000 genomes]
rs7668673	0.85[JPT][hapmap]
rs7670187	0.81[GIH][hapmap]
rs7672632	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9291121	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs9291122	0.84[ASN][1000 genomes]
rs9291123	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9790586	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs9999127	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][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	nsv878529	chr4:6883012-6983677	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4315786	GRPEL1	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6945000-6970200	Weak transcription	Hela-S3	cervix
2	chr4:6955800-6976000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:6956000-6976000	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:6957600-6970400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:6957600-6973800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:6957600-6976000	Weak transcription	Fetal Lung	lung
7	chr4:6957800-6976000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:6958400-6975800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr4:6964200-6976000	Weak transcription	Brain Germinal Matrix	brain
10	chr4:6964800-6973400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:6965000-6976000	Weak transcription	A549	lung
12	chr4:6965200-6970400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr4:6965200-6971600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:6965200-6973400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:6965200-6976000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr4:6965200-6976000	Weak transcription	Stomach Mucosa	stomach
17	chr4:6965200-6976200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:6965400-6969800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr4:6965400-6970000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:6965400-6973000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr4:6965400-6973000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:6965400-6973200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr4:6965400-6973400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr4:6965400-6973400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr4:6965400-6973600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:6965400-6974600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:6965400-6976000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:6965400-6976000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr4:6965400-6976000	Weak transcription	NHLF	lung
30	chr4:6965400-6976200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:6965400-6987800	Weak transcription	Small Intestine	intestine
32	chr4:6966200-6973800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:6966200-6976000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr4:6967000-6976000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr4:6967600-6973400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr4:6967600-6974400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr4:6967800-6973400	Weak transcription	Fetal Muscle Leg	muscle
38	chr4:6967800-6975000	Weak transcription	HSMMtube	muscle
39	chr4:6967800-6976000	Weak transcription	Fetal Kidney	kidney
40	chr4:6968000-6971600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr4:6968000-6973400	Weak transcription	Brain Angular Gyrus	brain
42	chr4:6968000-6987600	Weak transcription	HSMM	muscle
43	chr4:6968200-6976000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:6968400-6971400	Weak transcription	GM12878-XiMat	blood
45	chr4:6968400-6973400	Weak transcription	Brain Hippocampus Middle	brain
46	chr4:6968800-6971600	Strong transcription	HepG2	liver
47	chr4:6968800-6973800	Strong transcription	Primary T cells from cord blood	blood
48	chr4:6968800-6975000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr4:6968800-6975400	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr4:6969000-6969800	Strong transcription	Primary hematopoietic stem cells	blood

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