Variant report

Variant	rs6671782
Chromosome Location	chr1:174903762-174903763
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174899181..174902088-chr1:174902250..174905277,3	K562	blood:
2	chr1:174903721..174906103-chr1:174964849..174967396,3	K562	blood:

Variant related genes	Relation type
ENSG00000252552	Chromatin interaction

Extended variants
information (count: 158 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:156)

rs_ID	r²[population]
rs1012182	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10494492	0.80[EUR][1000 genomes]
rs10798324	0.84[EUR][1000 genomes]
rs10798327	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912843	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10912853	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912854	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10912855	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912857	0.85[EUR][1000 genomes]
rs11800350	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11806066	0.84[ASN][1000 genomes]
rs11809803	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11810508	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12063093	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12078839	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12094876	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1231826	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1231827	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1231829	0.92[ASN][1000 genomes]
rs1329281	0.83[EUR][1000 genomes]
rs1613634	0.87[EUR][1000 genomes]
rs1618207	0.82[EUR][1000 genomes]
rs1622802	0.83[EUR][1000 genomes]
rs1653630	0.88[EUR][1000 genomes]
rs1653634	0.85[EUR][1000 genomes]
rs16847335	0.81[EUR][1000 genomes]
rs16847337	0.81[EUR][1000 genomes]
rs16847624	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17302033	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1754350	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1754352	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1754353	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1754354	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17842156	0.82[EUR][1000 genomes]
rs17842157	0.81[EUR][1000 genomes]
rs1793292	0.85[EUR][1000 genomes]
rs1793294	0.85[EUR][1000 genomes]
rs1793295	0.83[EUR][1000 genomes]
rs1793298	0.87[EUR][1000 genomes]
rs1793305	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1793313	0.85[ASN][1000 genomes]
rs1793316	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1793318	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1793320	0.88[EUR][1000 genomes]
rs1813136	0.84[EUR][1000 genomes]
rs1883139	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1894198	0.92[ASN][1000 genomes]
rs1894199	0.95[ASN][1000 genomes]
rs1894201	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1894680	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1923818	0.83[EUR][1000 genomes]
rs193082	0.82[EUR][1000 genomes]
rs2003378	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2146564	0.82[EUR][1000 genomes]
rs2157541	0.85[EUR][1000 genomes]
rs2163628	0.85[EUR][1000 genomes]
rs2183202	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2568096	0.82[EUR][1000 genomes]
rs2568098	0.82[EUR][1000 genomes]
rs2760057	0.81[EUR][1000 genomes]
rs2771401	0.83[EUR][1000 genomes]
rs2860725	0.89[EUR][1000 genomes]
rs2861005	0.82[EUR][1000 genomes]
rs2861006	0.82[EUR][1000 genomes]
rs2981892	0.92[ASN][1000 genomes]
rs2981893	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2981896	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2987872	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2987873	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2987875	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2987876	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2987880	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3117838	0.83[EUR][1000 genomes]
rs3117843	0.81[EUR][1000 genomes]
rs3118982	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3118986	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3118987	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3118990	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs332767	0.83[EUR][1000 genomes]
rs332768	0.83[EUR][1000 genomes]
rs332779	0.83[EUR][1000 genomes]
rs332781	0.83[EUR][1000 genomes]
rs332782	0.83[EUR][1000 genomes]
rs332786	0.83[EUR][1000 genomes]
rs332793	0.81[EUR][1000 genomes]
rs332800	0.83[EUR][1000 genomes]
rs332801	0.83[EUR][1000 genomes]
rs333432	0.83[EUR][1000 genomes]
rs333436	0.82[EUR][1000 genomes]
rs36127331	0.81[EUR][1000 genomes]
rs3862941	0.81[EUR][1000 genomes]
rs392307	0.83[EUR][1000 genomes]
rs398350	0.83[EUR][1000 genomes]
rs458242	0.83[EUR][1000 genomes]
rs460878	0.82[EUR][1000 genomes]
rs464540	0.82[EUR][1000 genomes]
rs464635	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4651205	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4651231	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651235	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4652797	0.87[EUR][1000 genomes]
rs467437	0.83[EUR][1000 genomes]
rs55667039	0.81[EUR][1000 genomes]
rs55688014	0.82[EUR][1000 genomes]
rs55793234	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55844798	0.82[EUR][1000 genomes]
rs57289077	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58030712	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60482554	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60811893	0.82[EUR][1000 genomes]
rs6425298	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425300	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425301	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425303	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6425304	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6425306	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6670315	0.85[EUR][1000 genomes]
rs6671196	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671272	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6675528	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66836419	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684229	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684515	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686872	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6687616	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6690754	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6693979	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6696465	0.83[EUR][1000 genomes]
rs6700953	0.92[ASN][1000 genomes]
rs67054007	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67133776	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67203477	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67903803	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72715281	0.81[EUR][1000 genomes]
rs72715292	0.81[EUR][1000 genomes]
rs72715300	0.82[EUR][1000 genomes]
rs72717608	0.83[EUR][1000 genomes]
rs72717616	0.88[EUR][1000 genomes]
rs72717617	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72717618	0.89[EUR][1000 genomes]
rs72717630	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72717637	0.92[ASN][1000 genomes]
rs72717649	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72717650	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72717653	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717661	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717670	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7514183	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7516410	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521109	0.88[EUR][1000 genomes]
rs7543147	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7547658	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs913686	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs913688	0.89[EUR][1000 genomes]
rs9425787	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs989424	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	esv1794782	chr1:174900761-174925112	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6671782	MRPS14	Cis_1M	lymphoblastoid	RTeQTL
rs6671782	RP11-160H22.5	cis	Thyroid	GTEx
rs6671782	RABGAP1L	cis	Esophagus Muscularis	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174874000-174910000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:174874200-174938200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:174876800-174933600	Weak transcription	Aorta	Aorta
4	chr1:174886000-174907200	Weak transcription	Primary T cells from cord blood	blood
5	chr1:174886400-174911600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:174889600-174907400	Weak transcription	Primary B cells from cord blood	blood
7	chr1:174891800-174908600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:174892200-174905000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:174893400-174907600	Weak transcription	GM12878-XiMat	blood
10	chr1:174897400-174910000	Weak transcription	Gastric	stomach
11	chr1:174897800-174907200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:174898800-174910600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:174899800-174915200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:174900800-174904600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:174900800-174907600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:174900800-174907600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:174900800-174911000	Weak transcription	Brain Angular Gyrus	brain
18	chr1:174901000-174907800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:174901000-174909400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:174901000-174922200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:174901200-174905200	Weak transcription	Fetal Intestine Small	intestine
22	chr1:174901400-174907600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:174901600-174907200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:174901600-174907200	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:174901600-174907400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:174901800-174905000	Weak transcription	Fetal Intestine Large	intestine
27	chr1:174901800-174908000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:174902200-174909000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:174902600-174903800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:174902600-174907600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:174902600-174908400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr1:174903600-174904000	Enhancers	Pancreas	Pancrea

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