Variant report

Variant	rs17742611
Chromosome Location	chr4:7002344-7002345
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:6995184..6996770-chr4:7002166..7004163,2	K562	blood:
2	chr4:7000132..7002859-chr4:7044384..7046741,2	MCF-7	breast:
3	chr4:7001213..7003031-chr4:7014527..7016053,2	K562	blood:
4	chr4:6988801..6990522-chr4:7000909..7003794,2	MCF-7	breast:
5	chr4:6999677..7002587-chr4:7042055..7044238,2	K562	blood:
6	chr4:7001304..7003449-chr4:7034054..7035839,2	K562	blood:

Variant related genes	Relation type
ENSG00000173011	Chromatin interaction
ENSG00000132405	Chromatin interaction
ENSG00000173013	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10009332	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10013211	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10013696	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10015163	0.96[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10019256	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10019900	0.86[JPT][hapmap]
rs10022657	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[YRI][hapmap]
rs10022869	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10032908	0.92[CEU][hapmap];0.95[CHB][hapmap]
rs10155208	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10804990	0.90[JPT][hapmap]
rs10937762	0.83[GIH][hapmap];0.90[JPT][hapmap]
rs10937763	0.90[JPT][hapmap]
rs10937768	0.80[JPT][hapmap]
rs10937771	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10937778	0.81[CHB][hapmap]
rs10937779	0.80[CHB][hapmap]
rs11728984	0.86[JPT][hapmap]
rs11732389	0.86[JPT][hapmap]
rs12119	0.82[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs12512922	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12648134	0.82[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12650200	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12650264	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13140943	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17743234	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2301820	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2301821	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28380685	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34173965	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35490604	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35772786	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3857168	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3857169	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3857170	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3857172	0.84[ASN][1000 genomes]
rs3857173	0.82[ASN][1000 genomes]
rs3892145	0.96[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3892976	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41516949	0.86[JPT][hapmap]
rs4234790	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4315786	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]
rs4346651	0.81[JPT][hapmap]
rs4432749	0.85[JPT][hapmap]
rs4484301	0.96[CEU][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4608812	0.84[JPT][hapmap]
rs4689558	0.90[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs4689562	0.86[JPT][hapmap]
rs4689571	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4689572	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56307635	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6446552	0.86[JPT][hapmap]
rs6446553	0.86[JPT][hapmap]
rs6831368	0.81[JPT][hapmap]
rs6834007	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6848114	0.86[JPT][hapmap]
rs7670187	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs7672632	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9291121	0.86[JPT][hapmap]
rs9291123	0.86[JPT][hapmap]
rs9790586	0.81[JPT][hapmap]
rs9999127	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv34033	chr4:6973270-7390621	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757919	chr4:6988148-7269901	Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv2759221	chr4:6988148-7269901	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv428436	chr4:6988148-7269901	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv3358199	chr4:7000551-7004849	Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv593547	chr4:7002344-7032180	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17742611	GRPEL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6990400-7008800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:6991000-7021800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:6993200-7006800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:6993800-7008400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr4:6994000-7005200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:6994000-7008600	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr4:6994000-7035600	Strong transcription	Fetal Stomach	stomach
8	chr4:6994000-7043200	Weak transcription	Right Atrium	heart
9	chr4:6994200-7035400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:6994400-7013400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:6994600-7006800	Strong transcription	Stomach Smooth Muscle	stomach
12	chr4:6994600-7021400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:6994800-7007600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr4:6995000-7009200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:6995000-7020800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:6995200-7008400	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:6995200-7008600	Strong transcription	Fetal Intestine Small	intestine
18	chr4:6995400-7005000	Strong transcription	GM12878-XiMat	blood
19	chr4:6995400-7006600	Strong transcription	Duodenum Mucosa	Duodenum
20	chr4:6995400-7007800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr4:6995400-7008600	Strong transcription	Fetal Intestine Large	intestine
22	chr4:6995400-7013600	Strong transcription	Fetal Thymus	thymus
23	chr4:6995600-7006800	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr4:6995800-7003400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:6995800-7004200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:6995800-7006800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr4:6995800-7008200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:6995800-7008400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:6995800-7032800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:6996000-7004000	Strong transcription	Fetal Lung	lung
31	chr4:6996000-7004200	Weak transcription	Psoas Muscle	Psoas
32	chr4:6996000-7004600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:6996000-7006400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:6996000-7014800	Strong transcription	Primary B cells from peripheral blood	blood
35	chr4:6996000-7035200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr4:6996400-7007400	Strong transcription	Fetal Brain Female	brain
37	chr4:6996400-7034800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr4:6996600-7005000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:6996600-7005600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:6996600-7021400	Strong transcription	Brain Germinal Matrix	brain
41	chr4:6997600-7006400	Strong transcription	Left Ventricle	heart
42	chr4:6997800-7013800	Strong transcription	Thymus	Thymus
43	chr4:6998000-7006800	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr4:6998200-7004200	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr4:6998400-7004600	Strong transcription	NHLF	lung
46	chr4:6999000-7006800	Strong transcription	Lung	lung
47	chr4:6999800-7002400	Weak transcription	NH-A	brain
48	chr4:7000000-7004800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:7000000-7006400	Strong transcription	Colon Smooth Muscle	Colon
50	chr4:7000000-7006600	Strong transcription	Cortex derived primary cultured neurospheres	brain

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