Variant report

Variant	rs6425304
Chromosome Location	chr1:174881401-174881402
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1012182	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10798327	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10912843	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10912853	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10912854	0.87[AMR][1000 genomes]
rs10912855	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11800350	0.84[EUR][1000 genomes]
rs11809803	0.81[EUR][1000 genomes]
rs11810508	0.81[EUR][1000 genomes]
rs12063093	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12078839	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12094876	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1231826	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1231827	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16847624	0.82[EUR][1000 genomes]
rs17302033	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1754350	0.81[AMR][1000 genomes]
rs1754352	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1754353	0.80[EUR][1000 genomes]
rs1754354	0.81[EUR][1000 genomes]
rs1793305	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1793316	0.80[EUR][1000 genomes]
rs1883139	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1894201	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1894680	0.80[EUR][1000 genomes]
rs2860725	0.80[EUR][1000 genomes]
rs2981893	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2981896	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2987872	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2987873	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2987875	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2987876	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2987880	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3118982	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3118986	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3118987	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4651205	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4651231	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4651235	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55793234	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57289077	0.85[EUR][1000 genomes]
rs58030712	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60482554	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6425298	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6425300	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6425301	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6425303	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6425306	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6671196	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6671272	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6671782	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6675528	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs66836419	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6684229	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6684515	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6686872	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6687616	0.80[EUR][1000 genomes]
rs6690754	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6693979	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67054007	0.82[EUR][1000 genomes]
rs67133776	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67203477	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67903803	0.88[EUR][1000 genomes]
rs72717649	0.88[EUR][1000 genomes]
rs72717650	0.88[EUR][1000 genomes]
rs72717653	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72717661	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7514183	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7516410	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7543147	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7547658	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs913686	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs913688	0.80[EUR][1000 genomes]
rs9425787	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs989424	0.80[EUR][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
rs6425304	MRPS14	Cis_1M	lymphoblastoid	RTeQTL
rs6425304	RABGAP1L	cis	Esophagus Muscularis	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174861400-174902400	Weak transcription	Left Ventricle	heart
2	chr1:174862800-174882400	Weak transcription	Fetal Lung	lung
3	chr1:174863200-174883200	Weak transcription	Small Intestine	intestine
4	chr1:174863800-174883000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:174864200-174882000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:174871800-174882000	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:174872000-174885800	Weak transcription	Pancreas	Pancrea
8	chr1:174872000-174886000	Weak transcription	Gastric	stomach
9	chr1:174872000-174889200	Weak transcription	Primary B cells from cord blood	blood
10	chr1:174872200-174882600	Weak transcription	Stomach Mucosa	stomach
11	chr1:174872400-174888800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:174872800-174900400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:174873400-174897200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:174873600-174882000	Weak transcription	K562	blood
15	chr1:174874000-174910000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:174874200-174885400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:174874200-174885800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr1:174874200-174938200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:174874800-174882600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:174875400-174885400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:174876400-174882000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:174876800-174882600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:174876800-174933600	Weak transcription	Aorta	Aorta
24	chr1:174877200-174885600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:174877400-174883800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:174879200-174882200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:174879800-174885400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:174879800-174885400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:174880200-174885600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:174880800-174882200	Enhancers	GM12878-XiMat	blood
31	chr1:174881000-174881600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:174881000-174881600	Genic enhancers	Fetal Intestine Small	intestine
33	chr1:174881000-174882600	Enhancers	Fetal Intestine Large	intestine
34	chr1:174881200-174881800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:174881200-174881800	Enhancers	Fetal Brain Male	brain

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