Variant report

Variant	rs3764041
Chromosome Location	chr12:21489705-21489706
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr12:21489459-21490035	HepG2	liver:	n/a	chr12:21489749-21489764
2	FOXA1	chr12:21489635-21489897	T-47D	breast:	n/a	chr12:21489749-21489764
3	FOXA1	chr12:21489576-21490015	HepG2	liver:	n/a	chr12:21489749-21489764
4	TCF12	chr12:21489348-21490102	A549	lung:	n/a	chr12:21489754-21489763
5	MAX	chr12:21489663-21489753	HepG2	liver:	n/a	n/a
6	FOXA1	chr12:21489589-21489945	HepG2	liver:	n/a	chr12:21489749-21489764
7	FOXA1	chr12:21489630-21489925	T-47D	breast:	n/a	chr12:21489749-21489764
8	FOXA2	chr12:21489422-21490016	A549	lung:	n/a	n/a
9	FOXA1	chr12:21489550-21490018	HepG2	liver:	n/a	chr12:21489749-21489764
10	FOXA2	chr12:21489598-21489863	HepG2	liver:	n/a	n/a
11	FOXA2	chr12:21489572-21489954	A549	lung:	n/a	n/a
12	FOXA2	chr12:21489292-21490206	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:21489690-21489727	MCF10A-Er-Src	breast:	n/a	n/a
14	ARID3A	chr12:21489651-21489872	HepG2	liver:	n/a	n/a
15	SP1	chr12:21489438-21490055	A549	lung:	n/a	n/a
16	JUND	chr12:21489611-21489840	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:21488168..21491249-chr12:21492968..21494863,3	K562	blood:
2	chr12:21488168..21491197-chr12:21492551..21494863,3	K562	blood:

Variant related genes	Relation type
SLCO1A2	TF binding region

Extended variants
information (count: 140 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs10431251	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10459074	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs10459075	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs10505872	0.93[CEU][hapmap]
rs10743411	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10743412	0.98[ASN][1000 genomes]
rs10770795	0.92[ASN][1000 genomes]
rs10770796	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10770797	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs10841777	0.89[ASN][1000 genomes]
rs10841778	0.87[ASN][1000 genomes]
rs10841779	0.89[ASN][1000 genomes]
rs10841780	0.89[ASN][1000 genomes]
rs10841781	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs10841782	0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs10841786	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10841787	0.89[ASN][1000 genomes]
rs10841790	0.97[ASN][1000 genomes]
rs10841791	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs10841794	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11045919	0.93[CEU][hapmap]
rs11045922	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11045923	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs11045924	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs11045925	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11045927	0.93[CEU][hapmap]
rs11045929	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11045941	0.90[ASN][1000 genomes]
rs11045944	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11045948	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11045954	0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs11045955	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11045962	0.85[CHB][hapmap];0.93[ASN][1000 genomes]
rs11045965	0.96[ASN][1000 genomes]
rs11045966	0.95[ASN][1000 genomes]
rs11045967	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs11045968	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs11045969	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs11045970	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs11045971	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs11045974	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs11045975	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs11045976	0.99[ASN][1000 genomes]
rs11045980	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11533477	0.89[ASN][1000 genomes]
rs11535998	0.90[ASN][1000 genomes]
rs11536000	0.89[ASN][1000 genomes]
rs11537394	0.89[ASN][1000 genomes]
rs11561152	0.90[ASN][1000 genomes]
rs12227319	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12228765	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12230113	0.87[ASN][1000 genomes]
rs12230350	0.88[ASN][1000 genomes]
rs12230401	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12231212	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12231484	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs12231738	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12298817	0.93[CEU][hapmap]
rs12300594	0.93[CEU][hapmap]
rs12311809	0.86[ASN][1000 genomes]
rs12581287	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs12581327	0.89[ASN][1000 genomes]
rs16923597	0.93[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17333047	0.93[CEU][hapmap]
rs2127117	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2127118	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2169883	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2219791	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2219793	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[ASN][1000 genomes]
rs2306226	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2306227	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2306229	0.96[ASN][1000 genomes]
rs2306231	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2417971	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2417974	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs36089711	0.88[ASN][1000 genomes]
rs3736080	0.88[ASN][1000 genomes]
rs3736081	0.89[ASN][1000 genomes]
rs3751270	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs3764042	0.99[ASN][1000 genomes]
rs3764044	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs3764045	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs3794319	0.93[ASN][1000 genomes]
rs4078	0.93[CEU][hapmap]
rs4115170	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs4140389	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4148977	0.98[ASN][1000 genomes]
rs4148978	0.98[ASN][1000 genomes]
rs4148981	0.98[ASN][1000 genomes]
rs4148982	0.99[ASN][1000 genomes]
rs4148983	0.99[ASN][1000 genomes]
rs4148984	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4148985	0.99[ASN][1000 genomes]
rs4148986	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4148987	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4148988	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs4148989	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4148990	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4148991	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4148992	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4148993	0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs4148994	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4148995	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4148996	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4148997	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4148998	0.93[ASN][1000 genomes]
rs4148999	0.93[ASN][1000 genomes]
rs4149001	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4149002	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4149003	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4149004	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4149005	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4149006	0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4149007	0.86[ASN][1000 genomes]
rs4149008	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4149009	0.84[ASN][1000 genomes]
rs57899519	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6487216	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6487217	0.98[ASN][1000 genomes]
rs722994	0.93[CEU][hapmap]
rs7296472	0.80[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7300346	0.99[ASN][1000 genomes]
rs7300463	0.99[ASN][1000 genomes]
rs7305911	0.92[ASN][1000 genomes]
rs7313671	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs7315667	0.99[ASN][1000 genomes]
rs7955581	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7957203	0.99[ASN][1000 genomes]
rs7963398	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7967354	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7967935	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7968331	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7968842	0.99[ASN][1000 genomes]
rs7974575	0.93[CEU][hapmap]
rs7977517	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7977652	0.98[ASN][1000 genomes]
rs7978981	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7980842	0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs875234	0.93[EUR][1000 genomes];0.87[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	nsv557735	chr12:21443282-21538957	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3764041	CASC1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21485800-21492000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:21486600-21490600	Enhancers	Liver	Liver
3	chr12:21486800-21490000	Enhancers	Brain Substantia Nigra	brain
4	chr12:21487800-21491000	Weak transcription	Brain Angular Gyrus	brain
5	chr12:21488000-21489800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:21488400-21490000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:21488800-21489800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:21489000-21490200	Enhancers	Brain Hippocampus Middle	brain
9	chr12:21489600-21489800	Enhancers	Brain Anterior Caudate	brain
10	chr12:21489600-21490000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:21489600-21490000	Flanking Active TSS	Brain Cingulate Gyrus	brain
12	chr12:21489600-21490000	Enhancers	HepG2	liver
13	chr12:21489600-21490200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr12:21489600-21490200	Enhancers	A549	lung

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