Variant report

Variant	rs3124668
Chromosome Location	chr1:213184233-213184234
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:213184074..213185993-chr1:213223690..213226218,2	K562	blood:

Variant related genes	Relation type
ENSG00000136643	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10465694	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10864034	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11120080	0.81[EUR][1000 genomes]
rs1566247	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1976333	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1995151	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap]
rs2132428	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2172982	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2935209	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2935219	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2936010	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2936011	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3002284	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs3002285	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3010779	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3010780	0.84[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3010787	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3010789	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3123307	0.81[EUR][1000 genomes]
rs3738805	0.84[JPT][hapmap]
rs4543872	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951475	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951476	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4951479	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs4951662	0.84[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs6540778	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6657234	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6666814	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6671872	0.84[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs6691488	0.84[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6692144	0.84[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap]
rs6699158	0.85[AMR][1000 genomes];0.81[ASN][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	nsv1008594	chr1:213110654-213236750	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3124668	ANGEL2	cis	parietal	SCAN
rs3124668	RPS6KC1	cis	Artery Tibial	GTEx
rs3124668	LOC148696	cis	cerebellum	SCAN
rs3124668	ANGEL2	cis	cerebellum	SCAN
rs3124668	ANGEL2	cis	Esophagus Mucosa	GTEx
rs3124668	BATF3	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213154600-213187400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr1:213154800-213188000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:213154800-213188400	Weak transcription	Spleen	Spleen
4	chr1:213155600-213188000	Weak transcription	Aorta	Aorta
5	chr1:213155600-213188000	Weak transcription	Esophagus	oesophagus
6	chr1:213156200-213187400	Weak transcription	Fetal Brain Male	brain
7	chr1:213156200-213188000	Weak transcription	Pancreas	Pancrea
8	chr1:213158400-213188000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:213160200-213188000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:213160400-213187200	Weak transcription	NHLF	lung
11	chr1:213162000-213184600	Weak transcription	Psoas Muscle	Psoas
12	chr1:213162200-213188000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:213163200-213187400	Weak transcription	Stomach Mucosa	stomach
14	chr1:213167800-213187000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:213167800-213187000	Weak transcription	Fetal Heart	heart
16	chr1:213167800-213187800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:213169000-213186800	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:213169000-213187200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:213169000-213187800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:213169800-213186400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:213170000-213188000	Weak transcription	Colonic Mucosa	Colon
22	chr1:213170600-213187800	Weak transcription	Fetal Kidney	kidney
23	chr1:213173000-213186800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr1:213173000-213187000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:213177200-213187200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:213177400-213187800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:213177400-213188000	Weak transcription	Lung	lung
28	chr1:213178600-213188400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:213178800-213186600	Weak transcription	Brain Angular Gyrus	brain
30	chr1:213178800-213188000	Weak transcription	Gastric	stomach
31	chr1:213179200-213187400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:213179200-213187400	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:213179400-213185400	Weak transcription	HUVEC	blood vessel
34	chr1:213179400-213186400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr1:213179600-213187400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:213179600-213187400	Weak transcription	Brain Hippocampus Middle	brain
37	chr1:213179600-213187800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:213180200-213184400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr1:213180200-213188000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:213180400-213184600	Weak transcription	Fetal Brain Female	brain
41	chr1:213180400-213186400	Weak transcription	Brain Germinal Matrix	brain
42	chr1:213180400-213186400	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:213180400-213186800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr1:213180400-213187600	Weak transcription	Small Intestine	intestine
45	chr1:213180400-213188000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:213180400-213188000	Weak transcription	Fetal Stomach	stomach
47	chr1:213180600-213184400	Weak transcription	Brain Substantia Nigra	brain
48	chr1:213180600-213184400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:213180600-213186600	Weak transcription	Thymus	Thymus
50	chr1:213180600-213187400	Weak transcription	Right Ventricle	heart

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