Variant report

Variant	rs3773418
Chromosome Location	chr3:195006791-195006792
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	NFIC	chr3:195006734-195007342	SK-N-SH	brain:	n/a	n/a
2	JUND	chr3:195006675-195007463	T-47D	breast:	n/a	n/a
3	FOSL2	chr3:195006738-195007474	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr3:195006534-195007459	SK-N-SH	brain:	n/a	chr3:195006736-195006753 chr3:195007381-195007392 chr3:195006745-195006754
5	GATA2	chr3:195006617-195007332	HUVEC	blood vessel:	n/a	chr3:195006736-195006753 chr3:195006745-195006754
6	TCF12	chr3:195006757-195007440	SK-N-SH	brain:	n/a	chr3:195006880-195006888

No.	Distal block	Cell Line	Cell type
1	chr3:194990700..194993789-chr3:195004224..195007014,3	MCF-7	breast:
2	chr3:195006468..195008082-chr3:195243960..195245515,2	MCF-7	breast:
3	chr3:195002020..195004073-chr3:195005404..195007900,2	K562	blood:

Variant related genes	Relation type
ACAP2-IT1	TF binding region
ENSG00000173950	Chromatin interaction
ENSG00000229325	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10933706	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11718218	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11927933	0.80[ASN][1000 genomes]
rs13062574	0.93[ASN][1000 genomes]
rs1832667	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2050809	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2050810	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2410803	0.87[EUR][1000 genomes]
rs2410839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2410840	0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs28375276	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28688106	0.86[ASN][1000 genomes]
rs2898570	0.85[EUR][1000 genomes]
rs3087885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4677671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4677820	0.93[ASN][1000 genomes]
rs4677825	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4677830	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58204696	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437467	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6780743	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781643	0.92[EUR][1000 genomes]
rs6791601	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6791943	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792029	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6795263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73080837	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73080839	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7610022	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612694	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7638924	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7640100	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7643947	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7644002	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7649142	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823297	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs823299	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs823303	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823304	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823305	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs823307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823309	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs823312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs823313	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs823533	0.80[ASN][1000 genomes]
rs823534	0.80[ASN][1000 genomes]
rs862066	0.80[ASN][1000 genomes]
rs9288747	0.86[ASN][1000 genomes]
rs9831944	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9832920	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9863901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870813	1.00[JPT][hapmap]
rs9878312	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
5	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
6	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
7	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
12	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
13	nsv432510	chr3:194935314-195478861	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
14	nsv1005519	chr3:194964301-195340515	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
15	nsv432511	chr3:194986167-195479748	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3773418	ACAP2	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194992400-195009000	Weak transcription	Spleen	Spleen
2	chr3:194992600-195008200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:194992600-195008800	Weak transcription	Lung	lung
4	chr3:194992600-195090000	Weak transcription	Aorta	Aorta
5	chr3:194992800-195008600	Weak transcription	Ovary	ovary
6	chr3:194992800-195039800	Weak transcription	Fetal Brain Male	brain
7	chr3:194992800-195039800	Weak transcription	Right Ventricle	heart
8	chr3:194993000-195006800	Weak transcription	NHLF	lung
9	chr3:194993000-195007000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr3:194993000-195007000	Weak transcription	Brain Substantia Nigra	brain
11	chr3:194993000-195007200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:194993000-195007200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:194993000-195008200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:194993000-195008200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:194993000-195008800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:194993000-195009000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:194993000-195009600	Weak transcription	Fetal Kidney	kidney
18	chr3:194993000-195012800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:194993000-195020800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:194993000-195021400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:194993000-195038600	Weak transcription	Brain Hippocampus Middle	brain
22	chr3:194993000-195039200	Weak transcription	Brain Germinal Matrix	brain
23	chr3:194993000-195039600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:194993000-195050400	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:194993000-195076000	Weak transcription	Fetal Heart	heart
26	chr3:194993200-195006800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:194993200-195006800	Weak transcription	NHDF-Ad	bronchial
28	chr3:194993200-195007200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:194993200-195013000	Weak transcription	Hela-S3	cervix
30	chr3:194995000-195039800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr3:194995400-195008800	Weak transcription	K562	blood
32	chr3:194995400-195040000	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr3:194996200-195032200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:194996400-195033800	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr3:194996800-195008600	Weak transcription	Brain Angular Gyrus	brain
36	chr3:194997200-195027400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr3:194999200-195029400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr3:194999800-195008200	Weak transcription	Thymus	Thymus
39	chr3:195000000-195007400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:195000200-195007000	Weak transcription	Placenta	Placenta
41	chr3:195000400-195009000	Weak transcription	Colonic Mucosa	Colon
42	chr3:195001200-195016400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:195002200-195007000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:195002200-195007000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:195002200-195016600	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:195002200-195028200	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr3:195002600-195024000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:195002600-195024800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr3:195002600-195027400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:195003200-195017400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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