Variant report

Variant	rs6413827
Chromosome Location	chr1:173686353-173686354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:173686308..173688392-chr1:173689930..173692042,2	K562	blood:
2	chr1:173686216..173687823-chr1:173831086..173833729,2	K562	blood:
3	chr1:173685811..173687806-chr1:173687936..173689496,2	K562	blood:
4	chr1:173684233..173688038-chr1:173834072..173837696,4	K562	blood:
5	chr1:173682535..173686916-chr1:173792397..173795534,7	K562	blood:
6	chr1:173683067..173686676-chr1:173791976..173794755,4	K562	blood:
7	chr1:173680023..173685703-chr1:173685874..173692365,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000208317	Chromatin interaction
ENSG00000076321	Chromatin interaction
ENSG00000117593	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000120334	Chromatin interaction
ENSG00000270084	Chromatin interaction
ENSG00000185278	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10798290	0.90[CHB][hapmap]
rs10798295	0.81[MEX][hapmap]
rs10912651	0.84[CHB][hapmap]
rs10912670	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10912671	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];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12039524	0.85[CHB][hapmap]
rs12082131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12086229	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12561931	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12564699	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12565915	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12566945	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1322774	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs16846439	0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs1951625	0.89[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2067079	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2144708	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];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2208850	0.89[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2227612	0.90[CHB][hapmap]
rs2273366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2281486	0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.88[ASN][1000 genomes]
rs2295366	0.94[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs28804123	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3791020	0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.88[ASN][1000 genomes]
rs45467799	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4558043	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4652283	0.90[CHB][hapmap]
rs4652298	0.90[CHB][hapmap]
rs4652328	0.90[CHB][hapmap]
rs55633896	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55829688	0.88[ASN][1000 genomes]
rs56019876	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56048122	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56138893	0.94[ASN][1000 genomes]
rs56369162	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56928371	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57799150	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58287165	0.93[ASN][1000 genomes]
rs58825445	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs59858609	0.93[ASN][1000 genomes]
rs60264384	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61826805	0.94[ASN][1000 genomes]
rs61826806	0.94[ASN][1000 genomes]
rs61826809	0.94[ASN][1000 genomes]
rs61826810	0.94[ASN][1000 genomes]
rs61826812	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61826813	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61826821	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61826856	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61826857	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61827860	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61827861	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61827863	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61827865	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61827867	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61827870	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61827876	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61827877	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61827881	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61827925	0.88[ASN][1000 genomes]
rs6425251	0.90[CHB][hapmap]
rs6425253	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6425258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6425261	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6668702	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6673175	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674381	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6681766	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6691001	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6696680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7514556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7521884	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7530546	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7541082	0.90[CHB][hapmap]
rs7546048	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7548171	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7552741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7552939	0.81[MEX][hapmap]
rs9425416	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9425431	0.90[CHB][hapmap]
rs9425433	0.90[CHB][hapmap]
rs9425745	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9425756	0.94[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9660881	0.88[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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv1014827	chr1:173653453-173692470	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6413827	SLC9A11	cis	parietal	SCAN
rs6413827	DARS2	cis	Muscle Skeletal	GTEx
rs6413827	DARS2	cis	parietal	SCAN
rs6413827	RFWD2	cis	cerebellum	SCAN
rs6413827	DARS2	cis	Heart Left Ventricle	GTEx
rs6413827	DARS2	cis	cerebellum	SCAN
rs6413827	TNN	cis	parietal	SCAN
rs6413827	PRDX6	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173683400-173686600	Active TSS	GM12878-XiMat	blood
2	chr1:173684800-173687600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:173684800-173695000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:173684800-173702800	Weak transcription	Spleen	Spleen
5	chr1:173685000-173686400	Weak transcription	Gastric	stomach
6	chr1:173685000-173687200	Weak transcription	Lung	lung
7	chr1:173685000-173695200	Weak transcription	Esophagus	oesophagus
8	chr1:173685000-173695200	Weak transcription	Pancreas	Pancrea
9	chr1:173685000-173720800	Weak transcription	Small Intestine	intestine
10	chr1:173685200-173686400	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr1:173685200-173686400	Weak transcription	Ovary	ovary
12	chr1:173685200-173686400	Weak transcription	Right Ventricle	heart
13	chr1:173685200-173686600	Weak transcription	Stomach Mucosa	stomach
14	chr1:173685200-173686800	Enhancers	Brain Angular Gyrus	brain
15	chr1:173685200-173686800	Enhancers	Colon Smooth Muscle	Colon
16	chr1:173685200-173687000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:173685200-173687000	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr1:173685200-173687400	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr1:173685200-173687600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr1:173685200-173687800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:173685200-173687800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr1:173685200-173689400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:173685200-173690400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:173685200-173692200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:173685200-173692200	Weak transcription	Placenta	Placenta
26	chr1:173685200-173693400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:173685200-173694000	Weak transcription	Left Ventricle	heart
28	chr1:173685200-173694200	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:173685200-173694400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:173685200-173694400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr1:173685200-173694400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:173685200-173694400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:173685200-173694400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:173685200-173694600	Weak transcription	Colonic Mucosa	Colon
35	chr1:173685200-173724600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr1:173685400-173686400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:173685400-173686400	Weak transcription	Fetal Thymus	thymus
38	chr1:173685400-173686600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:173685400-173686600	Enhancers	Fetal Intestine Large	intestine
40	chr1:173685400-173686600	Enhancers	HSMM	muscle
41	chr1:173685400-173686800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr1:173685400-173686800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:173685400-173686800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:173685400-173686800	Enhancers	Adipose Nuclei	Adipose
45	chr1:173685400-173686800	Enhancers	Fetal Heart	heart
46	chr1:173685400-173686800	Enhancers	Rectal Smooth Muscle	rectum
47	chr1:173685400-173687000	Enhancers	Primary T cells from cord blood	blood
48	chr1:173685400-173687200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:173685400-173687200	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr1:173685400-173687200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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