Variant report

Variant	rs12375023
Chromosome Location	chr7:127553442-127553443
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127545052..127549084-chr7:127551154..127554840,4	K562	blood:
2	chr7:127552176..127555509-chr7:127561260..127564302,3	K562	blood:
3	chr7:127553227..127554781-chr7:127558910..127560585,2	K562	blood:
4	chr7:127549282..127550972-chr7:127552704..127555229,2	K562	blood:
5	chr7:127552472..127554151-chr7:127562624..127565296,2	MCF-7	breast:
6	chr7:127552933..127554693-chr7:127578388..127580537,2	MCF-7	breast:
7	chr7:127545052..127549084-chr7:127550970..127554840,5	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10487499	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487502	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154492	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12155421	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531847	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532894	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534918	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537331	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs12540357	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706816	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706818	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706819	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12706820	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706822	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706823	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13221709	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13227201	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13229973	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13231367	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236338	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246286	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345283	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1348103	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1362898	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419970	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468701	0.97[EUR][1000 genomes]
rs17151466	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151507	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151639	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs17151653	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151668	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151682	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151707	0.89[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs17151739	0.85[GIH][hapmap];0.93[MEX][hapmap]
rs17676654	1.00[ASN][1000 genomes]
rs34026100	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34688920	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34839191	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35154268	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41464647	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs55660321	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58406876	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58489175	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6467157	1.00[CHB][hapmap];0.85[GIH][hapmap];0.93[MEX][hapmap];1.00[ASN][1000 genomes]
rs67632185	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67827668	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948605	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953231	1.00[CHB][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6959487	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6962635	1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73232968	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73232972	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73234873	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73234874	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238078	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs741094	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7458839	0.97[EUR][1000 genomes]
rs7785596	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7805021	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809182	1.00[CEU][hapmap];0.85[GIH][hapmap];0.89[TSI][hapmap];0.97[EUR][1000 genomes]
rs7810024	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894062	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9649027	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9649512	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv526535	chr7:127445594-127623840	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1024743	chr7:127498695-127670004	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12375023	ARF5	cis	cerebellum	SCAN
rs12375023	HYAL4	cis	cerebellum	SCAN
rs12375023	SND1	cis	Artery Tibial	GTEx
rs12375023	GPR37	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127528800-127569200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr7:127529000-127557200	Weak transcription	Esophagus	oesophagus
3	chr7:127529200-127569400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr7:127532200-127569200	Weak transcription	Hela-S3	cervix
5	chr7:127532400-127569200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr7:127539000-127556400	Weak transcription	Psoas Muscle	Psoas
7	chr7:127541000-127569200	Weak transcription	Fetal Muscle Leg	muscle
8	chr7:127541200-127569400	Weak transcription	Left Ventricle	heart
9	chr7:127542800-127554200	Weak transcription	Gastric	stomach
10	chr7:127544800-127554400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:127544800-127560600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr7:127545000-127569200	Weak transcription	Thymus	Thymus
13	chr7:127545000-127569200	Weak transcription	HSMMtube	muscle
14	chr7:127545800-127555000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:127545800-127569200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr7:127546000-127566800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr7:127546200-127554200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr7:127546200-127559000	Weak transcription	HSMM	muscle
19	chr7:127546200-127560400	Weak transcription	Pancreas	Pancrea
20	chr7:127546200-127569200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr7:127546400-127558400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr7:127546400-127567400	Weak transcription	NHDF-Ad	bronchial
23	chr7:127546400-127569200	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr7:127546400-127569200	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr7:127546400-127569200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:127546400-127569200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr7:127546400-127569200	Weak transcription	Placenta	Placenta
28	chr7:127546400-127569200	Weak transcription	Dnd41	blood
29	chr7:127546800-127569000	Weak transcription	Fetal Thymus	thymus
30	chr7:127546800-127569200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr7:127546800-127569200	Weak transcription	Aorta	Aorta
32	chr7:127546800-127569200	Weak transcription	Lung	lung
33	chr7:127547400-127567000	Weak transcription	Liver	Liver
34	chr7:127547800-127569200	Weak transcription	Primary T cells from cord blood	blood
35	chr7:127547800-127569600	Weak transcription	A549	lung
36	chr7:127548000-127567000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr7:127548200-127555200	Weak transcription	Brain Substantia Nigra	brain
38	chr7:127548400-127560400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:127548400-127560600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr7:127548400-127562800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr7:127549200-127561000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr7:127549200-127567600	Weak transcription	NH-A	brain
43	chr7:127549800-127567400	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr7:127550000-127568000	Weak transcription	NHEK	skin
45	chr7:127551200-127553800	Enhancers	Primary B cells from peripheral blood	blood
46	chr7:127551200-127569400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr7:127551400-127554000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr7:127551400-127554000	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr7:127551400-127566800	Weak transcription	Small Intestine	intestine
50	chr7:127551400-127569200	Weak transcription	Primary T cells fromperipheralblood	blood

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