Variant report

Variant	rs229589
Chromosome Location	chr14:65262425-65262426
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	chr14:65255152..65259640-chr14:65260607..65263310,4	K562	blood:
2	chr14:65258140..65260514-chr14:65261209..65262960,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1271040	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs151165	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs1741466	0.83[CEU][hapmap];0.89[TSI][hapmap]
rs17767662	0.82[ASN][1000 genomes]
rs192036	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2038433	0.91[EUR][1000 genomes]
rs2269295	0.96[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2269296	0.96[CEU][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2269297	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs229580	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs229581	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs229586	0.83[JPT][hapmap]
rs229587	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs229588	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs229591	0.87[ASW][hapmap];0.96[CEU][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs229627	0.83[CEU][hapmap]
rs229628	0.87[CEU][hapmap]
rs229672	0.82[ASN][1000 genomes]
rs229673	0.97[CHD][hapmap];0.80[GIH][hapmap];0.82[ASN][1000 genomes]
rs229675	0.82[ASN][1000 genomes]
rs230703	0.82[TSI][hapmap]
rs230704	0.82[TSI][hapmap]
rs368194	0.83[CEU][hapmap];0.84[CHD][hapmap];0.88[TSI][hapmap]
rs3819928	0.87[EUR][1000 genomes]
rs433143	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4902317	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8017385	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1801406	chr14:65193725-65264416	Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
2	esv2757572	chr14:65254465-65271780	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv2759994	chr14:65254465-65271780	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs229589	CHURC1	cis	multi-tissue	Pritchard
rs229589	SIX6	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65228400-65265000	Weak transcription	Aorta	Aorta
2	chr14:65232200-65274200	Weak transcription	Gastric	stomach
3	chr14:65233000-65265600	Weak transcription	Fetal Brain Male	brain
4	chr14:65240400-65262800	Weak transcription	Brain Hippocampus Middle	brain
5	chr14:65244800-65272400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr14:65250400-65271800	Strong transcription	Fetal Muscle Leg	muscle
7	chr14:65251200-65267400	Weak transcription	Fetal Kidney	kidney
8	chr14:65251600-65264400	Weak transcription	Fetal Heart	heart
9	chr14:65252200-65265600	Weak transcription	Fetal Brain Female	brain
10	chr14:65252600-65274400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr14:65252800-65272600	Weak transcription	Psoas Muscle	Psoas
12	chr14:65254000-65282600	Weak transcription	Spleen	Spleen
13	chr14:65255600-65268800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr14:65257200-65271600	Strong transcription	Right Ventricle	heart
15	chr14:65257400-65263400	Strong transcription	Brain Germinal Matrix	brain
16	chr14:65257400-65267000	Strong transcription	Skeletal Muscle Male	skeletal muscle
17	chr14:65258000-65266800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr14:65258000-65274200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr14:65258200-65266800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr14:65258200-65271800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr14:65258400-65266800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr14:65258600-65272600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr14:65259000-65264200	Strong transcription	Left Ventricle	heart
24	chr14:65259400-65263400	Strong transcription	Pancreatic Islets	Pancreatic Islet
25	chr14:65259800-65266600	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr14:65260200-65262800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr14:65260400-65263600	Strong transcription	K562	blood
28	chr14:65262000-65270400	Weak transcription	Brain Anterior Caudate	brain
29	chr14:65262000-65289800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr14:65262200-65271800	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links