Variant report

Variant	rs11571396
Chromosome Location	chr12:1042103-1042104
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11571412	0.80[AFR][1000 genomes]
rs11571436	1.00[ASW][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs11571455	0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs11571464	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12320344	1.00[MEX][hapmap]
rs16931963	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16931987	0.92[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34880640	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869390	chr12:282465-1045994	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1049944	chr12:282465-1232077	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	nsv541306	chr12:282465-1232077	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv1044433	chr12:321619-1065402	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv541323	chr12:321619-1065402	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv949469	chr12:380411-1122450	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
7	nsv556890	chr12:662448-1100555	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
8	nsv556892	chr12:673515-1210884	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
9	nsv898576	chr12:813411-1553450	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
10	nsv948760	chr12:863833-1542875	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
11	nsv1042333	chr12:907975-1081509	Weak transcription Enhancers Strong transcription Flanking Active TSS 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 target site	16 gene(s)	inside rSNPs	diseases
12	nsv1052589	chr12:910460-1421493	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
13	nsv1045278	chr12:920251-1697030	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
14	nsv529398	chr12:941915-1741311	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
15	nsv468960	chr12:975276-1455106	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
16	nsv556941	chr12:975276-1455106	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
17	nsv1044329	chr12:985144-1403020	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
18	nsv541340	chr12:985144-1403020	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
19	nsv1041675	chr12:993822-1091354	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
20	nsv470256	chr12:998365-1438761	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
21	nsv492321	chr12:1011692-1388512	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
22	nsv898579	chr12:1013176-1510505	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
23	nsv898580	chr12:1024688-1569097	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats 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 miRNA target site	37 gene(s)	inside rSNPs	diseases
24	nsv1036488	chr12:1041097-1445923	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription 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	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11571396	LOC388796	trans	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:964400-1042200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:986200-1042200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:989200-1042200	Strong transcription	Fetal Muscle Leg	muscle
4	chr12:1020800-1054600	Strong transcription	Fetal Intestine Small	intestine
5	chr12:1024600-1055800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:1024800-1042200	Strong transcription	Fetal Thymus	thymus
7	chr12:1024800-1042200	Strong transcription	Dnd41	blood
8	chr12:1024800-1043200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:1024800-1057400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:1026000-1042200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:1026200-1043200	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr12:1026400-1042200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:1026400-1042400	Strong transcription	Fetal Stomach	stomach
14	chr12:1026400-1042600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr12:1026400-1048200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr12:1026600-1055800	Weak transcription	K562	blood
17	chr12:1029600-1042200	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr12:1029800-1042200	Strong transcription	Duodenum Mucosa	Duodenum
19	chr12:1029800-1042400	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:1030000-1042200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:1030000-1042600	Strong transcription	Fetal Muscle Trunk	muscle
22	chr12:1030200-1042400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr12:1030400-1042200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:1030400-1042200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:1030600-1042200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:1031200-1042200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:1031400-1042200	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr12:1032400-1042200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:1032400-1042200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:1032400-1042200	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr12:1032800-1042200	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr12:1033000-1042200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr12:1033000-1042200	Strong transcription	Brain Hippocampus Middle	brain
34	chr12:1033400-1042200	Strong transcription	Osteobl	bone
35	chr12:1033600-1042200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:1033600-1042200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr12:1033600-1042200	Strong transcription	Thymus	Thymus
38	chr12:1033600-1042400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:1033600-1042400	Strong transcription	A549	lung
40	chr12:1033600-1042400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr12:1033800-1042200	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr12:1034600-1042200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:1036400-1045400	Weak transcription	Fetal Heart	heart
44	chr12:1036600-1055200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr12:1037800-1042200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr12:1038400-1042200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr12:1038600-1042200	Strong transcription	Brain Anterior Caudate	brain
48	chr12:1038600-1042200	Strong transcription	NHEK	skin
49	chr12:1038800-1042200	Strong transcription	Primary hematopoietic stem cells	blood
50	chr12:1038800-1042800	Strong transcription	Primary B cells from cord blood	blood

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