Variant report

Variant	rs12063093
Chromosome Location	chr1:174862616-174862617
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:174861640..174863465-chr1:174967999..174970376,2	MCF-7	breast:
2	chr1:174861794..174864246-chr1:174865246..174868047,2	K562	blood:
3	chr1:174860980..174862757-chr1:174967700..174969508,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116161	Chromatin interaction
ENSG00000223525	Chromatin interaction

Extended variants
information (count: 180 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:179)

rs_ID	r²[population]
rs1012182	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1034462	0.81[ASN][1000 genomes]
rs10494492	0.81[EUR][1000 genomes]
rs1058741	0.81[ASN][1000 genomes]
rs10798324	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10798327	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912843	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912853	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912854	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10912855	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912857	0.84[EUR][1000 genomes]
rs11800350	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806066	0.89[ASN][1000 genomes]
rs11809803	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11810508	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12078839	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094876	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1231826	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1231827	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1231829	0.97[ASN][1000 genomes]
rs1329281	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1613634	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1618207	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1618408	0.82[ASN][1000 genomes]
rs1622802	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs162815	0.82[ASN][1000 genomes]
rs1653630	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1653634	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16847335	0.82[EUR][1000 genomes]
rs16847337	0.82[EUR][1000 genomes]
rs16847624	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17302033	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17302367	0.81[ASN][1000 genomes]
rs1754350	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1754352	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1754353	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1754354	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1754360	0.82[ASN][1000 genomes]
rs17842156	0.83[EUR][1000 genomes]
rs17842157	0.82[EUR][1000 genomes]
rs1793292	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1793294	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1793295	0.84[EUR][1000 genomes]
rs1793298	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1793305	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1793307	0.82[ASN][1000 genomes]
rs1793310	0.82[ASN][1000 genomes]
rs1793313	0.90[ASN][1000 genomes]
rs1793316	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1793318	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1793320	0.89[EUR][1000 genomes]
rs1813136	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1883139	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894198	0.97[ASN][1000 genomes]
rs1894199	1.00[ASN][1000 genomes]
rs1894201	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894680	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1923818	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs193082	0.82[EUR][1000 genomes]
rs2003378	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2060158	0.80[EUR][1000 genomes]
rs2146564	0.83[EUR][1000 genomes]
rs2157541	0.84[EUR][1000 genomes]
rs2157567	0.81[ASN][1000 genomes]
rs2163628	0.86[EUR][1000 genomes]
rs2183202	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2568096	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2568098	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2760057	0.82[EUR][1000 genomes]
rs2771401	0.84[EUR][1000 genomes]
rs2860725	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2861005	0.83[EUR][1000 genomes]
rs2861006	0.83[EUR][1000 genomes]
rs2981892	0.97[ASN][1000 genomes]
rs2981893	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2981896	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987872	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987873	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987875	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987876	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987880	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3117838	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3117843	0.82[EUR][1000 genomes]
rs3118982	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118986	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118987	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3118990	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs332767	0.83[EUR][1000 genomes]
rs332768	0.83[EUR][1000 genomes]
rs332779	0.84[EUR][1000 genomes]
rs332781	0.83[EUR][1000 genomes]
rs332782	0.83[EUR][1000 genomes]
rs332786	0.84[EUR][1000 genomes]
rs332793	0.82[EUR][1000 genomes]
rs332797	0.80[EUR][1000 genomes]
rs332800	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs332801	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs333422	0.83[EUR][1000 genomes]
rs333432	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs333436	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs333438	0.83[EUR][1000 genomes]
rs36127331	0.81[EUR][1000 genomes]
rs3766697	0.81[ASN][1000 genomes]
rs3862941	0.81[EUR][1000 genomes]
rs392307	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs398350	0.84[EUR][1000 genomes]
rs399530	0.83[EUR][1000 genomes]
rs411665	0.80[EUR][1000 genomes]
rs458242	0.84[EUR][1000 genomes]
rs459078	0.82[ASN][1000 genomes]
rs460878	0.83[EUR][1000 genomes]
rs464540	0.83[EUR][1000 genomes]
rs464635	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4651205	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4651231	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4651235	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652797	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs467437	0.84[EUR][1000 genomes]
rs55667039	0.81[EUR][1000 genomes]
rs55688014	0.83[EUR][1000 genomes]
rs55774740	0.81[ASN][1000 genomes]
rs55793234	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55844798	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57289077	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58030712	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60482554	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60811893	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6425298	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425300	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425301	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425303	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6425304	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6425306	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6670315	0.84[EUR][1000 genomes]
rs6671196	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6671272	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6671782	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6675528	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66836419	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6684229	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6684515	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6686872	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687616	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690754	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693979	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696465	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6700953	0.97[ASN][1000 genomes]
rs67054007	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67133776	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67203477	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67903803	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72715281	0.82[EUR][1000 genomes]
rs72715292	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72715294	0.84[ASN][1000 genomes]
rs72715300	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72717608	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72717616	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72717617	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72717618	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72717630	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717637	0.97[ASN][1000 genomes]
rs72717649	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72717650	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717653	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72717661	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72717670	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74128535	0.81[ASN][1000 genomes]
rs7514183	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7516410	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7521109	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7531032	0.81[ASN][1000 genomes]
rs7543147	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547658	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554767	0.81[ASN][1000 genomes]
rs913686	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs913687	0.82[ASN][1000 genomes]
rs913688	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9425787	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs989424	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12063093	RABGAP1L	cis	Esophagus Muscularis	GTEx
rs12063093	MRPS14	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174844800-174871600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:174844800-174874400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:174844800-174877400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:174845000-174862800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:174845000-174863000	Weak transcription	Primary T cells from cord blood	blood
6	chr1:174846600-174862800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:174846800-174874000	Weak transcription	Ovary	ovary
8	chr1:174847000-174869200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:174847400-174862800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:174847400-174863000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:174847400-174864400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:174847400-174864600	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr1:174847400-174864600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:174847600-174874400	Weak transcription	Esophagus	oesophagus
15	chr1:174849200-174864400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:174849600-174864400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:174850200-174874800	Weak transcription	Fetal Stomach	stomach
18	chr1:174850400-174869600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:174852000-174873400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:174852800-174864000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:174852800-174874800	Weak transcription	Spleen	Spleen
22	chr1:174853400-174865000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:174853400-174870200	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr1:174854000-174862800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:174854200-174862800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:174856600-174866600	Weak transcription	Primary B cells from cord blood	blood
27	chr1:174856800-174876400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:174857000-174870800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:174857000-174871200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:174857800-174867200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr1:174858000-174871200	Weak transcription	Lung	lung
32	chr1:174859000-174868600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:174859000-174874000	Weak transcription	Brain Angular Gyrus	brain
34	chr1:174859400-174863000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:174859400-174866600	Weak transcription	Gastric	stomach
36	chr1:174859600-174867200	Weak transcription	HepG2	liver
37	chr1:174859600-174873400	Weak transcription	K562	blood
38	chr1:174860200-174868200	Weak transcription	Fetal Heart	heart
39	chr1:174861200-174863600	Strong transcription	GM12878-XiMat	blood
40	chr1:174861400-174864400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:174861400-174866600	Weak transcription	Pancreas	Pancrea
42	chr1:174861400-174871200	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr1:174861400-174876200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:174861400-174902400	Weak transcription	Left Ventricle	heart
45	chr1:174862400-174864200	Enhancers	Fetal Intestine Small	intestine
46	chr1:174862400-174864400	Enhancers	Fetal Intestine Large	intestine
47	chr1:174862600-174862800	Enhancers	Fetal Lung	lung
48	chr1:174862600-174863000	Weak transcription	Small Intestine	intestine
49	chr1:174862600-174863400	Enhancers	Duodenum Mucosa	Duodenum
50	chr1:174862600-174863600	Enhancers	Stomach Mucosa	stomach

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