Variant report

Variant	rs396000
Chromosome Location	chr6:109519611-109519612
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	chr6:108881031..108883166-chr6:109519450..109522215,2	K562	blood:
2	chr6:109518100..109519817-chr6:109760825..109763676,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118689	Chromatin interaction
ENSG00000135587	Chromatin interaction
ENSG00000185250	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10447414	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1111863	0.81[CEU][hapmap]
rs1111865	0.81[CEU][hapmap]
rs1111866	0.81[CEU][hapmap]
rs11153168	0.80[CEU][hapmap]
rs1146246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12176068	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1260593	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1260594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1260595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1260596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1269172	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1271697	0.83[EUR][1000 genomes]
rs13196590	0.84[CEU][hapmap]
rs13200047	0.80[CEU][hapmap]
rs1341272	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1521908	0.81[CEU][hapmap]
rs171272	0.83[EUR][1000 genomes]
rs173288	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1741921	0.82[EUR][1000 genomes]
rs1741930	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]
rs1761608	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][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];0.99[ASN][1000 genomes]
rs1766814	0.83[EUR][1000 genomes]
rs2483913	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34527629	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs351724	0.92[CEU][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs351725	0.92[CEU][hapmap];0.85[YRI][hapmap];0.86[EUR][1000 genomes]
rs351728	0.92[CEU][hapmap]
rs351742	0.84[CEU][hapmap];0.82[GIH][hapmap];0.83[EUR][1000 genomes]
rs351743	0.82[EUR][1000 genomes]
rs351745	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs351748	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs351749	0.83[EUR][1000 genomes]
rs351752	0.83[EUR][1000 genomes]
rs351754	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs351755	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs351756	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs352837	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs368467	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]
rs371960	0.84[CEU][hapmap];0.81[GIH][hapmap];0.83[EUR][1000 genomes]
rs378447	0.83[EUR][1000 genomes]
rs380774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381565	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs386696	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs392820	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs398944	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs399561	0.84[CEU][hapmap];0.82[GIH][hapmap];0.83[EUR][1000 genomes]
rs419106	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419998	0.82[EUR][1000 genomes]
rs427960	0.84[CEU][hapmap];0.82[GIH][hapmap];0.83[EUR][1000 genomes]
rs435090	0.81[AMR][1000 genomes]
rs435611	0.83[EUR][1000 genomes]
rs437779	0.84[EUR][1000 genomes]
rs440849	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs442405	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs4427037	0.90[JPT][hapmap]
rs445796	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs449850	0.84[CEU][hapmap];0.82[GIH][hapmap];0.83[EUR][1000 genomes]
rs455839	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs458185	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs458740	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs459956	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs4601178	0.81[CEU][hapmap]
rs461487	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs463503	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs463916	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs670414	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6903107	0.91[JPT][hapmap]
rs6919423	0.92[CEU][hapmap]
rs6924815	0.84[CEU][hapmap]
rs7755970	0.91[JPT][hapmap]
rs7772602	0.81[CEU][hapmap]
rs7774390	0.90[JPT][hapmap]
rs932223	0.91[JPT][hapmap]
rs9374069	0.90[JPT][hapmap]
rs9374070	0.91[JPT][hapmap]
rs9374071	0.91[JPT][hapmap]
rs9374072	0.91[JPT][hapmap]
rs9384703	0.91[JPT][hapmap]
rs9384704	0.91[JPT][hapmap]
rs9386780	0.91[JPT][hapmap]
rs9386781	0.90[JPT][hapmap]
rs9386784	0.91[JPT][hapmap]
rs9386790	0.81[CEU][hapmap]
rs9398188	0.83[EUR][1000 genomes]
rs9398191	0.91[JPT][hapmap]
rs9398192	0.91[JPT][hapmap]
rs9400269	0.81[CEU][hapmap]
rs9480910	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9480921	0.81[CEU][hapmap]
rs9480922	0.80[CEU][hapmap]
rs9480923	0.81[CEU][hapmap]
rs9487003	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9487033	0.81[CEU][hapmap]
rs9487034	0.81[CEU][hapmap]
rs949881	0.91[JPT][hapmap]
rs949882	0.91[JPT][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs396000	ZBTB24	cis	parietal	SCAN
rs396000	GSTM2P1	cis	parietal	SCAN
rs396000	CD164	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109516400-109535000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr6:109517200-109544800	Weak transcription	Psoas Muscle	Psoas
3	chr6:109518400-109520400	Enhancers	Pancreas	Pancrea
4	chr6:109518600-109520000	Weak transcription	Stomach Mucosa	stomach

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