Variant report

Variant	rs12089230
Chromosome Location	chr1:212263217-212263218
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	chr1:212260403..212263243-chr1:212265417..212267031,2	K562	blood:
2	chr1:212263201..212265024-chr1:212267233..212269275,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10863936	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11119836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11119843	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12066042	0.85[EUR][1000 genomes]
rs12070369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12076757	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1387814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1387815	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17656163	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17656362	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17656453	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17699790	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17700264	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2358333	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2358440	0.82[JPT][hapmap]
rs2884428	0.87[YRI][hapmap]
rs2970595	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3010023	0.82[JPT][hapmap]
rs4093392	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4394721	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951560	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4951561	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4951567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55806741	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55960291	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56289586	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56292525	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61828530	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61828533	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61828539	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61828543	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61828547	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61830761	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6657728	0.82[JPT][hapmap];0.81[LWK][hapmap];0.87[YRI][hapmap]
rs6666948	0.87[CEU][hapmap]
rs6675660	0.83[EUR][1000 genomes]
rs66858610	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67417805	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7519826	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7525895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7547097	0.85[CEU][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	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12089230	ATF3	cis	cerebellum	SCAN
rs12089230	HHAT	cis	parietal	SCAN
rs12089230	INTS7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212214400-212278000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:212229600-212266600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:212229800-212266400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:212230000-212265200	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:212233000-212266400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:212234000-212265400	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:212234000-212265800	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:212234200-212267400	Strong transcription	Dnd41	blood
9	chr1:212236000-212265200	Strong transcription	K562	blood
10	chr1:212237000-212266200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:212237200-212267000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:212237600-212266800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:212241600-212264200	Weak transcription	Fetal Brain Female	brain
14	chr1:212241600-212284600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr1:212244600-212267200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:212249400-212266000	Strong transcription	A549	lung
17	chr1:212253000-212270800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:212254800-212278000	Weak transcription	NHDF-Ad	bronchial
19	chr1:212256000-212266600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr1:212256000-212266800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:212256000-212271000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:212256400-212264800	Weak transcription	HepG2	liver
23	chr1:212256400-212265800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:212256400-212271200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:212256400-212278600	Weak transcription	NHLF	lung
26	chr1:212259400-212264600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:212261000-212263400	Genic enhancers	Fetal Thymus	thymus
28	chr1:212261000-212263400	Enhancers	Right Atrium	heart
29	chr1:212261000-212264800	Enhancers	Fetal Heart	heart
30	chr1:212261000-212265200	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr1:212261200-212263400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr1:212261200-212263600	Enhancers	Primary T cells from cord blood	blood
33	chr1:212261200-212264400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:212261600-212263400	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr1:212261800-212263600	Enhancers	Primary B cells from cord blood	blood
36	chr1:212261800-212263600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:212261800-212264600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr1:212261800-212271800	Weak transcription	Spleen	Spleen
39	chr1:212262000-212265200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:212262000-212266400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:212262000-212266400	Weak transcription	Fetal Stomach	stomach
42	chr1:212262000-212266600	Weak transcription	HSMM	muscle
43	chr1:212262000-212266800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:212262000-212271800	Weak transcription	Hela-S3	cervix
45	chr1:212262000-212276800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:212262000-212283000	Weak transcription	NH-A	brain
47	chr1:212262000-212284400	Weak transcription	Osteobl	bone
48	chr1:212262200-212264800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:212262200-212266600	Weak transcription	Thymus	Thymus
50	chr1:212262200-212272200	Weak transcription	Gastric	stomach

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