Variant report

Variant	rs12024897
Chromosome Location	chr1:169339268-169339269
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169337822..169339719-chr1:169451874..169454199,3	K562	blood:
2	chr1:169073561..169077593-chr1:169336088..169341683,7	K562	blood:
3	chr1:169338121..169342264-chr1:169451874..169455112,4	K562	blood:
4	chr1:169337259..169338842-chr1:169338923..169340546,3	MCF-7	breast:
5	chr1:169338197..169339910-chr1:169345261..169347920,2	MCF-7	breast:
6	chr1:169275275..169277238-chr1:169338409..169341241,2	K562	blood:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction
ENSG00000117475	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10429893	0.85[CEU][hapmap]
rs10458395	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10458396	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10458397	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489187	0.81[ASN][1000 genomes]
rs10489188	0.81[ASN][1000 genomes]
rs10800439	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10800441	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800446	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919154	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919155	0.81[ASN][1000 genomes]
rs10919163	0.81[ASN][1000 genomes]
rs10919164	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919167	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1112839	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11799936	0.81[ASN][1000 genomes]
rs11799948	0.81[ASN][1000 genomes]
rs11800843	0.86[CHB][hapmap];0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs11808015	0.81[ASN][1000 genomes]
rs12021770	0.81[ASN][1000 genomes]
rs12022776	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12026287	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12026728	0.81[ASN][1000 genomes]
rs12026996	0.86[CHB][hapmap]
rs12027242	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12028813	0.81[ASN][1000 genomes]
rs12029853	0.86[CHB][hapmap]
rs12030320	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs12032201	0.81[ASN][1000 genomes]
rs12033253	0.86[CHB][hapmap]
rs12034986	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12037211	0.86[CHB][hapmap]
rs12038609	0.86[CHB][hapmap]
rs12043489	0.86[CHB][hapmap]
rs12049227	0.81[ASN][1000 genomes]
rs12563090	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1400836	0.85[CEU][hapmap]
rs1415928	0.86[CHB][hapmap]
rs1517748	0.97[ASN][1000 genomes]
rs1589113	0.86[CHB][hapmap]
rs16862118	0.81[ASN][1000 genomes]
rs16862172	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs1980198	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2003652	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003654	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2014061	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235195	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs2268048	0.86[CHB][hapmap]
rs2275299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28566091	0.81[ASN][1000 genomes]
rs35269183	0.81[ASN][1000 genomes]
rs3753303	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766089	0.86[CHB][hapmap]
rs3766095	0.85[CEU][hapmap]
rs3766096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3905328	0.85[CEU][hapmap]
rs4656183	0.82[CEU][hapmap]
rs4656670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4656672	0.85[CEU][hapmap]
rs61807018	0.81[ASN][1000 genomes]
rs6427185	0.85[CEU][hapmap]
rs6427186	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427188	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6427189	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6427191	0.81[ASN][1000 genomes]
rs6660945	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677410	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690801	0.81[ASN][1000 genomes]
rs6696428	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696810	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72702179	0.81[ASN][1000 genomes]
rs72702188	0.81[ASN][1000 genomes]
rs7516248	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7528375	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528449	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7535788	0.81[ASN][1000 genomes]
rs7537890	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7539415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554703	0.96[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs961404	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9659035	0.81[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	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12024897	CELF6	trans	cerebellum	SCAN
rs12024897	BLZF1	cis	Whole Blood	GTEx
rs12024897	C1orf114	cis	cerebellum	SCAN
rs12024897	NME7	cis	Thyroid	GTEx
rs12024897	F5	cis	cerebellum	SCAN
rs12024897	SELP	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169338000-169340000	Weak transcription	Left Ventricle	heart
2	chr1:169338000-169351200	Weak transcription	Lung	lung
3	chr1:169338000-169351200	Weak transcription	Spleen	Spleen
4	chr1:169338000-169353600	Weak transcription	Small Intestine	intestine
5	chr1:169338000-169358000	Weak transcription	Esophagus	oesophagus
6	chr1:169338000-169360000	Weak transcription	Fetal Heart	heart
7	chr1:169338000-169360400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:169338000-169365200	Weak transcription	Gastric	stomach
9	chr1:169338000-169365600	Weak transcription	Pancreas	Pancrea
10	chr1:169338200-169339400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:169338200-169339400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr1:169338200-169340600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:169338200-169341200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:169338200-169341600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:169338200-169345800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr1:169338200-169345800	Weak transcription	Ovary	ovary
17	chr1:169338200-169351800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr1:169338200-169360400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:169338200-169360400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:169338200-169362200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:169338200-169363600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:169338200-169363600	Weak transcription	Stomach Mucosa	stomach
23	chr1:169338200-169369000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:169338400-169345800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:169338400-169345800	Weak transcription	Right Ventricle	heart
26	chr1:169338400-169349600	Weak transcription	HSMMtube	muscle
27	chr1:169338400-169360200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:169338400-169362600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:169338600-169339400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:169338600-169339400	Enhancers	HepG2	liver
31	chr1:169338600-169339600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:169338600-169340400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:169338600-169341600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:169338600-169341800	Weak transcription	Fetal Kidney	kidney
35	chr1:169338600-169345800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:169338600-169345800	Weak transcription	Colonic Mucosa	Colon
37	chr1:169338600-169345800	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:169338600-169345800	Weak transcription	Psoas Muscle	Psoas
39	chr1:169338600-169346000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:169338600-169346000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr1:169338600-169349800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:169338600-169351400	Weak transcription	Thymus	Thymus
43	chr1:169338600-169352200	Weak transcription	Aorta	Aorta
44	chr1:169338600-169352200	Weak transcription	Fetal Stomach	stomach
45	chr1:169338600-169352400	Weak transcription	Fetal Intestine Small	intestine
46	chr1:169338600-169352800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:169338600-169357600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:169338800-169339400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:169338800-169339400	Genic enhancers	Hela-S3	cervix
50	chr1:169338800-169339400	Enhancers	HUVEC	blood vessel

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