Variant report

Variant	rs12573024
Chromosome Location	chr10:91453618-91453619
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:91452973..91455330-chr10:91459934..91462307,2	K562	blood:
2	chr10:91452372..91455010-chr10:91457256..91459357,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PANK1-2	chr10:91451057-91454559	XLOC_008897

Variant related genes	Relation type
ENSG00000240996	Chromatin interaction
ENSG00000138182	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10159610	0.92[CEU][hapmap]
rs10430645	0.87[GIH][hapmap];0.80[JPT][hapmap]
rs10430646	0.80[JPT][hapmap]
rs1048057	0.80[GIH][hapmap]
rs10509579	0.87[GIH][hapmap];0.80[JPT][hapmap]
rs1062465	0.87[GIH][hapmap];0.80[JPT][hapmap]
rs10785896	0.80[JPT][hapmap]
rs10881618	0.87[GIH][hapmap];0.80[JPT][hapmap]
rs10881631	0.80[JPT][hapmap]
rs10881666	0.87[GIH][hapmap];0.89[JPT][hapmap]
rs11185841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11185861	0.80[JPT][hapmap]
rs11185880	0.81[JPT][hapmap]
rs11598411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11817267	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12250365	0.80[GIH][hapmap]
rs12414170	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12569886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12570256	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12571525	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12573060	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12766537	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326260	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1409355	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1409358	0.87[GIH][hapmap];0.80[JPT][hapmap]
rs1555868	0.80[JPT][hapmap]
rs1555881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555882	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886997	0.87[GIH][hapmap];0.80[JPT][hapmap]
rs2026550	0.80[JPT][hapmap]
rs2038920	1.00[CEU][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2077946	0.87[GIH][hapmap]
rs2420640	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3740037	0.87[GIH][hapmap];0.80[JPT][hapmap]
rs3824609	0.87[GIH][hapmap];0.80[JPT][hapmap]
rs4934493	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56189305	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6586218	0.80[JPT][hapmap]
rs7076259	0.87[GIH][hapmap];0.80[JPT][hapmap]
rs7076351	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];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7081362	0.80[JPT][hapmap]
rs7085805	0.80[JPT][hapmap]
rs7087240	0.80[JPT][hapmap]
rs7089150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7089473	0.80[JPT][hapmap]
rs7089645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7092444	0.87[GIH][hapmap];0.80[JPT][hapmap]
rs7095818	0.87[GIH][hapmap];0.80[JPT][hapmap]
rs7096466	0.87[GIH][hapmap];0.80[JPT][hapmap]
rs7097496	0.80[JPT][hapmap]
rs7098988	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100603	0.87[GIH][hapmap];0.80[JPT][hapmap]
rs716781	0.80[JPT][hapmap]
rs745215	0.88[EUR][1000 genomes]
rs749607	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7895379	0.87[GIH][hapmap];0.80[JPT][hapmap]
rs7898670	0.80[JPT][hapmap]
rs7905382	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7910615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7911443	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7912591	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8181361	0.87[GIH][hapmap];0.80[JPT][hapmap]
rs9325443	0.87[GIH][hapmap];0.80[JPT][hapmap]
rs943127	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs962524	0.87[GIH][hapmap];0.80[JPT][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12573024	KIF20B	cis	cerebellum	SCAN
rs12573024	FLJ37201	cis	parietal	SCAN
rs12573024	KIF20B	cis	parietal	SCAN
rs12573024	FGFBP3	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91444600-91460800	Weak transcription	Left Ventricle	heart
2	chr10:91444800-91455000	Weak transcription	NHEK	skin
3	chr10:91445200-91460600	Weak transcription	Fetal Muscle Leg	muscle
4	chr10:91447200-91459800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr10:91453000-91460600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr10:91453400-91459400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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