Variant report

Variant	rs481196
Chromosome Location	chr12:57826133-57826134
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57820715..57827591-chr12:57847165..57857509,18	K562	blood:
2	chr12:57824494..57826362-chr12:57997412..57999477,2	K562	blood:
3	chr12:57822828..57827240-chr12:57828141..57836129,12	MCF-7	breast:
4	chr12:57821945..57826454-chr12:57843844..57847049,4	K562	blood:
5	chr12:57822750..57826133-chr12:57852904..57855936,4	K562	blood:
6	chr12:57824473..57826346-chr12:57880233..57882392,2	MCF-7	breast:
7	chr12:57825005..57827571-chr12:57912550..57914471,2	K562	blood:
8	chr12:57821945..57831494-chr12:57839441..57852842,32	K562	blood:
9	chr12:57734197..57736239-chr12:57824447..57826782,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000175197	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000179912	Chromatin interaction
ENSG00000178498	Chromatin interaction
ENSG00000175189	Chromatin interaction
ENSG00000111087	Chromatin interaction
ENSG00000139269	Chromatin interaction
ENSG00000166986	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10747777	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs10747778	1.00[CEU][hapmap]
rs10783818	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs10783819	1.00[CEU][hapmap]
rs10876976	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs10876977	0.83[EUR][1000 genomes]
rs10876978	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10876980	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10876981	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10876983	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172156	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs11172169	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11172170	1.00[CEU][hapmap]
rs11172190	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172191	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172205	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11172211	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11172214	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172222	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11609986	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs12230111	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12296766	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs12310220	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs12369598	0.80[ASN][1000 genomes]
rs12423654	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12579911	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12812140	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1284252	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1798710	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2063778	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2280139	1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28504983	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3923885	1.00[CEU][hapmap];0.93[GIH][hapmap];0.97[TSI][hapmap]
rs4075325	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs4108243	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4760228	0.85[EUR][1000 genomes]
rs4760236	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs4760244	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4760305	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4760306	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4760308	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs4760348	1.00[CEU][hapmap]
rs491750	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs492749	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs512223	0.85[EUR][1000 genomes]
rs533975	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs537482	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs543410	0.81[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs560048	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs568793	0.86[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs575153	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6581131	1.00[CEU][hapmap]
rs6581134	0.81[ASW][hapmap];0.93[GIH][hapmap]
rs6581136	1.00[CEU][hapmap]
rs7132367	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7133939	1.00[CEU][hapmap]
rs7135142	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs7298418	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs7303070	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7307059	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs7309659	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap]
rs7398058	1.00[CEU][hapmap]
rs7486863	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs7977908	1.00[CEU][hapmap]
rs7980310	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9738004	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs481196	SP7	cis	parietal	SCAN
rs481196	KIAA0748	cis	cerebellum	SCAN
rs481196	KIF5A	cis	cerebellum	SCAN
rs481196	TSPAN31	cis	cerebellum	SCAN
rs481196	KRT81	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57824200-57826200	Active TSS	Liver	Liver
2	chr12:57825000-57828600	Weak transcription	Gastric	stomach
3	chr12:57825200-57828400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:57825200-57828600	Weak transcription	Pancreas	Pancrea
5	chr12:57825400-57826200	Enhancers	Primary T cells fromperipheralblood	blood
6	chr12:57825400-57828000	Weak transcription	Fetal Muscle Leg	muscle
7	chr12:57825400-57828200	Weak transcription	Placenta	Placenta
8	chr12:57825400-57828400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:57825400-57828400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:57825400-57828400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:57825400-57828400	Weak transcription	Fetal Stomach	stomach
12	chr12:57825400-57828600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:57825400-57828800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:57825400-57828800	Weak transcription	Fetal Thymus	thymus
15	chr12:57825400-57829000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:57825600-57826400	Enhancers	Fetal Intestine Small	intestine
17	chr12:57825600-57828000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:57825600-57828200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr12:57825600-57828200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:57825600-57828600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr12:57825600-57848600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr12:57825800-57826400	Enhancers	Dnd41	blood
23	chr12:57825800-57827800	Weak transcription	HepG2	liver
24	chr12:57825800-57828000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr12:57825800-57828000	Weak transcription	A549	lung
26	chr12:57825800-57828400	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr12:57825800-57828400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:57825800-57828600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr12:57825800-57828800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr12:57825800-57828800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:57826000-57828000	Weak transcription	Fetal Intestine Large	intestine
32	chr12:57826000-57828400	Weak transcription	K562	blood

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