Variant report

Variant	rs6446220
Chromosome Location	chr3:50825303-50825304
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CISH-3	chr3:50825005-50825716	NONHSAT089856

Extended variants
information (count: 165 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:165)

rs_ID	r²[population]
rs1013233	0.81[AFR][1000 genomes]
rs10510754	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130255	0.94[CEU][hapmap]
rs11130263	0.94[CEU][hapmap]
rs11130267	0.94[CEU][hapmap]
rs11710858	0.94[CEU][hapmap]
rs11712367	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11917538	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11921011	0.94[CEU][hapmap]
rs11928733	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12639126	0.94[CEU][hapmap]
rs12639243	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13065995	0.94[CEU][hapmap]
rs13069365	0.82[CEU][hapmap]
rs13075377	0.94[CEU][hapmap]
rs13079136	0.94[CEU][hapmap]
rs13079565	0.94[CEU][hapmap]
rs13085827	0.94[CEU][hapmap]
rs13086922	0.94[CEU][hapmap]
rs13088434	0.94[CEU][hapmap]
rs13093798	0.94[CEU][hapmap]
rs13094785	0.94[CEU][hapmap]
rs13095920	0.94[CEU][hapmap]
rs13096264	0.94[CEU][hapmap]
rs13096772	0.94[CEU][hapmap]
rs1379875	0.94[CEU][hapmap]
rs1385025	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs1458385	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1458386	0.94[CEU][hapmap]
rs1458387	0.94[CEU][hapmap]
rs1463496	0.94[CEU][hapmap]
rs1463497	0.94[CEU][hapmap]
rs1471177	0.94[CEU][hapmap]
rs1531271	0.94[CEU][hapmap]
rs1598926	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs175634	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs17660513	0.93[CEU][hapmap]
rs1824280	0.94[CEU][hapmap]
rs1824281	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1947607	0.94[CEU][hapmap]
rs1966920	0.94[CEU][hapmap]
rs1971976	0.84[AFR][1000 genomes]
rs2045510	0.94[CEU][hapmap]
rs2045511	0.94[CEU][hapmap]
rs2061388	0.94[CEU][hapmap]
rs2085580	0.94[CEU][hapmap]
rs2085582	0.94[CEU][hapmap]
rs2125366	0.94[CEU][hapmap]
rs2125369	0.94[CEU][hapmap]
rs2168863	0.94[CEU][hapmap]
rs2168866	0.94[CEU][hapmap]
rs2199050	0.94[CEU][hapmap]
rs2219431	0.94[CEU][hapmap]
rs2219432	0.94[CEU][hapmap]
rs2219433	0.94[CEU][hapmap]
rs2262810	0.94[CEU][hapmap]
rs2355323	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs2355350	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2355697	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2355700	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2355702	0.94[CEU][hapmap]
rs2608988	0.94[CEU][hapmap]
rs2609001	0.94[CEU][hapmap]
rs2609006	0.94[CEU][hapmap]
rs2609020	0.94[CEU][hapmap]
rs2609022	0.94[CEU][hapmap]
rs2609024	0.94[CEU][hapmap]
rs2609031	0.94[CEU][hapmap]
rs2609036	0.94[CEU][hapmap]
rs2609037	0.94[CEU][hapmap]
rs2675772	0.94[CEU][hapmap]
rs2675773	0.94[CEU][hapmap]
rs2675792	0.94[CEU][hapmap]
rs2675806	0.94[CEU][hapmap]
rs2675810	0.88[CEU][hapmap]
rs2675812	0.94[CEU][hapmap]
rs2675816	0.91[CEU][hapmap]
rs2675830	0.94[CEU][hapmap]
rs2675832	0.94[CEU][hapmap]
rs2675834	0.94[CEU][hapmap]
rs2675835	0.94[CEU][hapmap]
rs2675836	0.94[CEU][hapmap]
rs2675837	0.94[CEU][hapmap]
rs2883652	0.94[CEU][hapmap]
rs34628582	0.94[CEU][hapmap]
rs34848480	0.82[AFR][1000 genomes]
rs375544	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs3792325	0.94[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap]
rs3792328	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs3804628	0.94[CEU][hapmap]
rs3943212	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes]
rs396302	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs4132022	0.88[CEU][hapmap]
rs414171	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4346541	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4346542	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs441516	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs4429624	0.94[CEU][hapmap]
rs443436	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs4447760	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs448028	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs4482663	0.93[CEU][hapmap]
rs4485709	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes]
rs4530518	0.92[CEU][hapmap]
rs453570	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs4688702	0.94[CEU][hapmap]
rs61108141	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs616589	0.94[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.97[YRI][hapmap]
rs6446212	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs6446213	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs6446214	0.88[CEU][hapmap]
rs6446222	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6446243	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6446245	0.82[EUR][1000 genomes]
rs6769733	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6771085	0.94[CEU][hapmap]
rs6775012	0.93[CEU][hapmap]
rs6776224	0.93[CEU][hapmap]
rs6778680	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs6779819	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs6791880	0.94[CEU][hapmap]
rs6795573	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6796769	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs6810241	0.94[CEU][hapmap]
rs728901	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.81[AFR][1000 genomes]
rs7433217	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs751851	0.82[AFR][1000 genomes]
rs7611428	0.94[CEU][hapmap]
rs7614482	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7615703	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7616183	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7621650	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7627266	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7629253	0.94[CEU][hapmap]
rs7638082	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7639301	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7639828	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7642158	0.94[CEU][hapmap]
rs7646236	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs7650574	0.94[CEU][hapmap]
rs7652715	0.94[CEU][hapmap]
rs808149	0.81[AFR][1000 genomes]
rs809451	0.94[CEU][hapmap]
rs813243	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs900735	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs936405	0.94[CEU][hapmap]
rs936406	0.94[CEU][hapmap]
rs9682401	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs9820606	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9823942	0.94[CEU][hapmap]
rs9824444	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9824522	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9825535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9826757	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9831288	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9832952	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9838283	0.94[CEU][hapmap]
rs9838433	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9839684	0.92[CEU][hapmap]
rs9859692	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9867489	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9868870	0.94[CEU][hapmap]
rs9869945	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9875961	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9877272	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6446220	HEMK1	cis	Lymphoblastoid	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50819400-50825600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:50821000-50825600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:50821200-50827400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:50823400-50825800	Weak transcription	Brain Anterior Caudate	brain
5	chr3:50824400-50825800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:50824400-50826000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:50824400-50826600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:50824400-50829600	Weak transcription	Brain Angular Gyrus	brain
9	chr3:50824600-50826600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:50824800-50826200	Enhancers	Brain Cingulate Gyrus	brain
11	chr3:50825200-50825400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr3:50825200-50825600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:50825200-50825800	Enhancers	HUES48 Cell Line	embryonic stem cell

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