Variant report

Variant	rs6424944
Chromosome Location	chr1:184266177-184266178
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:184259867..184262376-chr1:184264911..184267175,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1006198	0.88[EUR][1000 genomes]
rs10442605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10797946	0.81[EUR][1000 genomes]
rs10911531	0.81[EUR][1000 genomes]
rs10911553	0.83[ASN][1000 genomes]
rs10911554	0.83[ASN][1000 genomes]
rs10911555	0.91[CHB][hapmap]
rs1111088	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11576933	0.83[ASN][1000 genomes]
rs11585071	0.82[CHB][hapmap]
rs11806061	0.88[EUR][1000 genomes]
rs12120085	0.93[EUR][1000 genomes]
rs12136077	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12139516	0.81[EUR][1000 genomes]
rs12139721	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1327139	0.80[AFR][1000 genomes]
rs1327147	0.88[AFR][1000 genomes]
rs1409809	0.82[AFR][1000 genomes]
rs1571972	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1831055	0.80[AFR][1000 genomes]
rs1831056	0.80[AFR][1000 genomes]
rs1854086	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1930290	0.83[ASN][1000 genomes]
rs2216932	0.93[EUR][1000 genomes]
rs2378825	0.82[AFR][1000 genomes]
rs2378841	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2840274	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4306092	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4428848	0.91[CHB][hapmap]
rs4650663	0.80[EUR][1000 genomes]
rs4650664	0.93[EUR][1000 genomes]
rs4651193	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4651195	0.93[EUR][1000 genomes]
rs4651197	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4651199	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4651200	0.91[CHB][hapmap]
rs4651201	0.84[ASW][hapmap]
rs6424933	0.82[AFR][1000 genomes]
rs6424934	0.82[AFR][1000 genomes]
rs6424940	0.93[EUR][1000 genomes]
rs6666447	0.83[ASN][1000 genomes]
rs6678460	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6684740	0.83[ASN][1000 genomes]
rs6695243	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697326	0.99[ASN][1000 genomes]
rs7522326	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522468	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7530243	1.00[CHB][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs7554776	0.86[ASN][1000 genomes]
rs932993	0.87[CHB][hapmap]
rs963234	0.91[CHB][hapmap]
rs9787399	0.91[CHB][hapmap]

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	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6424944	TMEM177	cis	Liver	GTEx
rs6424944	NMNAT2	cis	cerebellum	SCAN
rs6424944	RGL1	cis	parietal	SCAN
rs6424944	RALGPS2	cis	parietal	SCAN
rs6424944	TMEM177	trans	multi-tissue	Pritchard

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184255600-184266400	Weak transcription	Spleen	Spleen
2	chr1:184258600-184267400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:184259600-184266400	Weak transcription	Pancreas	Pancrea
4	chr1:184261600-184268000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:184263400-184266200	Enhancers	Fetal Heart	heart
6	chr1:184264600-184266400	Enhancers	Primary hematopoietic stem cells	blood
7	chr1:184264600-184269400	Enhancers	Fetal Brain Female	brain
8	chr1:184264800-184266800	Enhancers	Aorta	Aorta
9	chr1:184264800-184269600	Enhancers	Fetal Brain Male	brain
10	chr1:184264800-184269800	Enhancers	Fetal Muscle Leg	muscle
11	chr1:184265000-184267600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:184265000-184269200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr1:184265200-184266400	Weak transcription	Lung	lung
14	chr1:184265200-184266600	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr1:184265200-184267000	Enhancers	Dnd41	blood
16	chr1:184265200-184268200	Enhancers	Osteobl	bone
17	chr1:184265200-184268400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:184265200-184269000	Enhancers	Fetal Stomach	stomach
19	chr1:184265200-184269200	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr1:184265200-184270600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:184265200-184271800	Enhancers	NHLF	lung
22	chr1:184265400-184266200	Enhancers	Rectal Smooth Muscle	rectum
23	chr1:184265400-184266400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:184265400-184266400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:184265400-184266400	Enhancers	Brain Cingulate Gyrus	brain
26	chr1:184265400-184266400	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr1:184265400-184266400	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr1:184265400-184266600	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr1:184265400-184266800	Enhancers	Fetal Lung	lung
30	chr1:184265400-184267000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr1:184265400-184267000	Enhancers	Adipose Nuclei	Adipose
32	chr1:184265400-184267400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:184265400-184269400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:184265600-184266200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:184265600-184266200	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr1:184265600-184266200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:184265600-184266200	Enhancers	Brain Hippocampus Middle	brain
38	chr1:184265600-184266200	Enhancers	HSMMtube	muscle
39	chr1:184265600-184266400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:184265600-184266600	Enhancers	Gastric	stomach
41	chr1:184265600-184266800	Enhancers	HSMM	muscle
42	chr1:184265600-184267000	Enhancers	Colon Smooth Muscle	Colon
43	chr1:184265800-184266200	Flanking Active TSS	HUVEC	blood vessel
44	chr1:184265800-184266200	Enhancers	NHDF-Ad	bronchial
45	chr1:184265800-184266400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr1:184265800-184266400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr1:184265800-184266400	Enhancers	Stomach Mucosa	stomach
48	chr1:184265800-184266600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:184265800-184266600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:184265800-184266600	Enhancers	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links