Variant report

Variant	rs12650200
Chromosome Location	chr4:7021170-7021171
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7019880..7022246-chr4:7042172..7045634,3	K562	blood:
2	chr4:7021136..7024360-chr4:7026095..7028817,3	K562	blood:
3	chr4:7019569..7021853-chr4:7034145..7036760,2	MCF-7	breast:
4	chr4:6927466..6930094-chr4:7020098..7022400,2	MCF-7	breast:
5	chr4:7019555..7022636-chr4:7025338..7028522,3	K562	blood:
6	chr4:7015008..7018342-chr4:7019176..7022360,4	K562	blood:
7	chr4:7016710..7019332-chr4:7019618..7021338,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173011	Chromatin interaction
ENSG00000173013	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10007295	0.81[EUR][1000 genomes]
rs10009332	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10013211	0.92[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10013696	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10015163	0.96[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10019256	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10022657	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs10022869	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10032908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs10155208	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10937762	0.81[GIH][hapmap]
rs10937771	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10937777	0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs10937778	0.86[CHB][hapmap]
rs10937779	0.85[CHB][hapmap]
rs12119	0.89[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs12512922	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12648134	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12650264	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13140943	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17742611	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]
rs17743234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2301820	0.89[CEU][hapmap];0.90[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2301821	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28380685	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34173965	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35490604	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35772786	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756255	0.82[CHB][hapmap]
rs3857168	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3857169	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3857170	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3857173	0.81[ASN][1000 genomes]
rs3892145	0.96[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3892976	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4234790	0.84[AMR][1000 genomes]
rs4315786	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]
rs4484301	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4689558	0.83[MEX][hapmap]
rs4689571	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4689572	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56307635	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6834007	0.82[AMR][1000 genomes]
rs7670187	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7672632	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9999127	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
7	nsv469847	chr4:7003525-7168441	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv878531	chr4:7006541-7129556	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv878532	chr4:7010504-7055603	Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS 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 target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12650200	GRPEL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6991000-7021800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:6994000-7035600	Strong transcription	Fetal Stomach	stomach
3	chr4:6994000-7043200	Weak transcription	Right Atrium	heart
4	chr4:6994200-7035400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:6994600-7021400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:6995800-7032800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:6996000-7035200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:6996400-7034800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:6996600-7021400	Strong transcription	Brain Germinal Matrix	brain
10	chr4:7000200-7021600	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr4:7000600-7034400	Strong transcription	Dnd41	blood
12	chr4:7001400-7034600	Strong transcription	Primary T cells from cord blood	blood
13	chr4:7001600-7035200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr4:7001600-7035400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr4:7001800-7029000	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr4:7001800-7035000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr4:7002000-7034400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr4:7002200-7035400	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr4:7002400-7034400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr4:7003600-7032600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr4:7006600-7021800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:7007600-7022000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:7008000-7022200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:7008200-7022000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:7008200-7034600	Strong transcription	Fetal Brain Female	brain
26	chr4:7008200-7035200	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr4:7008400-7022800	Strong transcription	NHEK	skin
28	chr4:7008400-7035400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:7008400-7035400	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr4:7008800-7035000	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:7009800-7021600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:7009800-7035200	Strong transcription	Fetal Intestine Large	intestine
33	chr4:7009800-7035600	Strong transcription	Duodenum Mucosa	Duodenum
34	chr4:7010000-7021200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:7010000-7021200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:7010000-7022200	Weak transcription	Hela-S3	cervix
37	chr4:7010000-7034600	Strong transcription	Adipose Nuclei	Adipose
38	chr4:7010200-7024400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:7010200-7032600	Weak transcription	Stomach Mucosa	stomach
40	chr4:7010400-7021400	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr4:7010400-7021600	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr4:7010800-7021400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr4:7010800-7035000	Strong transcription	Esophagus	oesophagus
44	chr4:7011200-7024400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr4:7011600-7036600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr4:7011600-7043600	Weak transcription	Psoas Muscle	Psoas
47	chr4:7013200-7044400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr4:7014200-7032800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr4:7014400-7034400	Strong transcription	Fetal Thymus	thymus
50	chr4:7014600-7021200	Strong transcription	Gastric	stomach

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