Variant report

Variant	rs11168455
Chromosome Location	chr12:48592792-48592793
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48549910..48551454-chr12:48590661..48592818,2	K562	blood:
2	chr12:48549661..48552655-chr12:48590661..48593368,4	K562	blood:
3	chr12:48590039..48593666-chr12:48742360..48744824,3	K562	blood:
4	chr12:48366898..48369197-chr12:48592697..48594577,2	K562	blood:
5	chr12:48510785..48513717-chr12:48592045..48593630,2	K562	blood:
6	chr12:48576960..48580173-chr12:48592129..48594089,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167528	Chromatin interaction
ENSG00000177875	Chromatin interaction
ENSG00000177981	Chromatin interaction
ENSG00000152556	Chromatin interaction
ENSG00000257735	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1018973	0.81[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs10492080	0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs1074174	0.81[CHB][hapmap]
rs10783231	0.81[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10783232	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783233	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783237	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10783239	0.85[AMR][1000 genomes]
rs11168449	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11168451	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11609399	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11612578	0.91[JPT][hapmap]
rs11613485	0.80[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs12822085	0.87[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1476608	0.81[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs1489111	0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap]
rs17122565	0.87[GIH][hapmap];0.91[JPT][hapmap]
rs17122612	0.81[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs17122651	0.80[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs1859441	0.84[TSI][hapmap]
rs1968071	0.81[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs2013956	0.84[AMR][1000 genomes]
rs2054902	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs2258342	0.93[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs2409001	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2634679	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs2634699	0.86[CHB][hapmap]
rs2732455	0.93[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs2732458	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs2732477	0.93[CEU][hapmap];0.85[CHB][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap]
rs2732487	0.93[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs3742074	0.81[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs4075913	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4141065	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4760611	0.92[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs4760620	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4760623	0.85[AMR][1000 genomes]
rs4760683	0.81[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs4760685	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs4760692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760698	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580653	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6580656	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6580657	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6580660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs726354	0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs7294641	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7296913	0.83[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs7305418	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7312326	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs7313023	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7315258	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7485057	0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7485824	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs757556	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7953726	0.85[AMR][1000 genomes]
rs7959755	0.80[CEU][hapmap]
rs7963934	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs7967762	0.81[TSI][hapmap]
rs7969749	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7971668	0.81[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs879242	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs901962	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs901963	0.81[CEU][hapmap];0.82[GIH][hapmap]
rs901964	0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11168455	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48590800-48593000	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr12:48591000-48592800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr12:48591000-48593000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:48591000-48593000	Active TSS	Duodenum Mucosa	Duodenum
5	chr12:48591000-48593200	Active TSS	Right Ventricle	heart
6	chr12:48591200-48592800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr12:48591200-48592800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:48591200-48592800	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr12:48591200-48592800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr12:48591200-48592800	Active TSS	Psoas Muscle	Psoas
11	chr12:48591200-48592800	Active TSS	Hela-S3	cervix
12	chr12:48591200-48593000	Active TSS	Colon Smooth Muscle	Colon
13	chr12:48591200-48593000	Flanking Active TSS	Osteobl	bone
14	chr12:48591200-48593200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr12:48591200-48593200	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr12:48591200-48593200	Active TSS	Left Ventricle	heart
17	chr12:48591200-48593200	Active TSS	NHDF-Ad	bronchial
18	chr12:48591200-48593400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr12:48591200-48594200	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr12:48591400-48592800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr12:48591400-48592800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:48591400-48592800	Active TSS	Ovary	ovary
23	chr12:48591400-48592800	Active TSS	A549	lung
24	chr12:48591400-48592800	Active TSS	HSMM	muscle
25	chr12:48591400-48592800	Active TSS	HSMMtube	muscle
26	chr12:48591400-48593000	Active TSS	H9 Cell Line	embryonic stem cell
27	chr12:48591400-48593000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:48591400-48593000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:48591400-48593000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:48591400-48593000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr12:48591400-48593000	Active TSS	Brain Germinal Matrix	brain
32	chr12:48591400-48593000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:48591400-48593000	Active TSS	Esophagus	oesophagus
34	chr12:48591400-48593000	Active TSS	Fetal Brain Female	brain
35	chr12:48591400-48593200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
36	chr12:48591400-48593200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:48591400-48593200	Active TSS	Brain Angular Gyrus	brain
38	chr12:48591400-48593200	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr12:48591400-48593200	Active TSS	Brain Substantia Nigra	brain
40	chr12:48591400-48593200	Active TSS	Thymus	Thymus
41	chr12:48591400-48593400	Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr12:48591400-48593400	Active TSS	Brain Anterior Caudate	brain
43	chr12:48591400-48593400	Active TSS	Brain Cingulate Gyrus	brain
44	chr12:48591400-48593600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:48591400-48594000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr12:48591600-48592800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr12:48591600-48592800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:48591600-48592800	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr12:48591600-48592800	Active TSS	Fetal Intestine Large	intestine
50	chr12:48591600-48592800	Active TSS	Gastric	stomach

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