Variant report

Variant	rs12488979
Chromosome Location	chr3:195033876-195033877
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:195028253..195031997-chr3:195032734..195036397,6	K562	blood:
2	chr3:195032015..195035498-chr3:195161704..195164752,3	K562	blood:
3	chr3:195026519..195030688-chr3:195031134..195036189,5	K562	blood:

Variant related genes	Relation type
ENSG00000114331	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs11919965	1.00[CHB][hapmap]
rs12485302	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12485380	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12485407	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12485433	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12485787	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12486168	1.00[CHB][hapmap]
rs12486220	1.00[CHB][hapmap]
rs12486241	0.93[AMR][1000 genomes]
rs12486536	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12486636	1.00[CHB][hapmap];0.82[MEX][hapmap]
rs12486805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12486835	1.00[CHB][hapmap]
rs12487670	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12487961	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12488451	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12488481	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12488562	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12488616	1.00[CHB][hapmap]
rs12488869	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12489090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12489620	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12489849	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12490460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes]
rs12490658	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12491026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12491371	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12491581	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12491670	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12491736	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12491788	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12491808	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.93[AMR][1000 genomes]
rs12491854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes]
rs12492552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12492644	0.80[AMR][1000 genomes]
rs12494306	0.80[AMR][1000 genomes]
rs12494564	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12494759	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12494773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12494820	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12494883	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12495657	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12496202	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496204	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496885	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12497178	0.93[AMR][1000 genomes]
rs12497478	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12497671	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12497677	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12497906	1.00[CHB][hapmap];0.82[MEX][hapmap]
rs1808074	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2029707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes]
rs2050807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2050808	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34643420	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35419807	0.93[AMR][1000 genomes]
rs3773419	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3773420	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3796161	1.00[CHB][hapmap];0.82[MEX][hapmap]
rs41266981	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41266999	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41267003	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56211708	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60040536	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6767801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6777904	1.00[CHB][hapmap]
rs6798243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6804467	1.00[CHB][hapmap]
rs72499627	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72607893	0.90[AMR][1000 genomes]
rs72607894	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72607895	0.96[AMR][1000 genomes]
rs72607896	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72607897	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72607898	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72607899	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72607900	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72607901	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72607902	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72611103	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs755202	1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.90[AMR][1000 genomes]
rs7642127	1.00[CHB][hapmap]
rs7653179	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs999331	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv432512	chr3:195007260-195475989	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12488979	FAM43A	cis	lymphoblastoid	seeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194992600-195090000	Weak transcription	Aorta	Aorta
2	chr3:194992800-195039800	Weak transcription	Fetal Brain Male	brain
3	chr3:194992800-195039800	Weak transcription	Right Ventricle	heart
4	chr3:194993000-195038600	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:194993000-195039200	Weak transcription	Brain Germinal Matrix	brain
6	chr3:194993000-195039600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:194993000-195050400	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:194993000-195076000	Weak transcription	Fetal Heart	heart
9	chr3:194995000-195039800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr3:194995400-195040000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr3:195004000-195039600	Weak transcription	Pancreas	Pancrea
12	chr3:195004000-195066600	Weak transcription	Small Intestine	intestine
13	chr3:195004200-195039600	Weak transcription	Gastric	stomach
14	chr3:195005200-195039600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:195008000-195039800	Weak transcription	NH-A	brain
16	chr3:195010000-195039000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:195010000-195039600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:195010000-195039800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:195010000-195039800	Weak transcription	Brain Substantia Nigra	brain
20	chr3:195010000-195061000	Weak transcription	Fetal Kidney	kidney
21	chr3:195010000-195076400	Weak transcription	Brain Angular Gyrus	brain
22	chr3:195013200-195039400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr3:195014200-195040800	Weak transcription	Hela-S3	cervix
24	chr3:195016000-195039600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:195016200-195039800	Weak transcription	NHLF	lung
26	chr3:195016400-195038600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr3:195018200-195034200	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr3:195019400-195034000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr3:195021800-195039600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:195021800-195039600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:195022600-195038600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr3:195022600-195073400	Weak transcription	HMEC	breast
33	chr3:195022800-195038600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:195022800-195039600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:195022800-195039600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:195022800-195039600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:195022800-195039800	Weak transcription	Colonic Mucosa	Colon
38	chr3:195022800-195073400	Weak transcription	NHEK	skin
39	chr3:195023000-195038200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:195023000-195038600	Weak transcription	Fetal Lung	lung
41	chr3:195023000-195039600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr3:195023000-195039600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:195023000-195039800	Weak transcription	HepG2	liver
44	chr3:195023000-195040200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:195023400-195039400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:195024000-195039600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:195024200-195039600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:195024400-195035600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:195024600-195039600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:195024600-195039600	Weak transcription	Esophagus	oesophagus

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