Variant report

Variant	rs2369494
Chromosome Location	chr12:1147834-1147835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:1098834..1102191-chr12:1145986..1148768,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000002016	Chromatin interaction
ENSG00000250132	Chromatin interaction
ENSG00000082805	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10773922	1.00[AMR][1000 genomes]
rs10773923	0.90[LWK][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10849618	0.80[ASW][hapmap];1.00[MEX][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes]
rs1544424	1.00[AMR][1000 genomes]
rs2097860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4604948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4765690	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap]
rs4765691	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6489777	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap]
rs6489778	1.00[AMR][1000 genomes]
rs7972852	1.00[AMR][1000 genomes]
rs933338	0.81[ASW][hapmap];0.81[LWK][hapmap];1.00[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	nsv1037825	chr12:1045734-1432940	Bivalent/Poised TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
19	nsv541342	chr12:1045734-1432940	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers 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	33 gene(s)	inside rSNPs	diseases
20	nsv868854	chr12:1045935-1354083	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
21	esv2762958	chr12:1049279-1554962	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
22	nsv1052559	chr12:1077964-1588543	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS 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	29 gene(s)	inside rSNPs	diseases
23	nsv898581	chr12:1084783-1527359	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
24	nsv1041799	chr12:1091294-1304839	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
25	nsv541343	chr12:1091294-1304839	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
26	nsv468963	chr12:1106783-1220688	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
27	nsv556943	chr12:1106783-1220688	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2369494	WNT5B	cis	lymphoblastoid	seeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1113400-1157000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr12:1128800-1154800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:1128800-1157200	Weak transcription	Psoas Muscle	Psoas
4	chr12:1128800-1157200	Weak transcription	HSMMtube	muscle
5	chr12:1128800-1162600	Weak transcription	Fetal Heart	heart
6	chr12:1130000-1152800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:1131800-1152800	Weak transcription	A549	lung
8	chr12:1135600-1152600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:1135600-1153400	Weak transcription	HSMM	muscle
10	chr12:1136000-1148200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:1136200-1153000	Weak transcription	NHDF-Ad	bronchial
12	chr12:1137000-1156000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr12:1137600-1152600	Weak transcription	NHLF	lung
14	chr12:1137600-1157000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr12:1137600-1157600	Weak transcription	Esophagus	oesophagus
16	chr12:1137600-1162200	Weak transcription	Spleen	Spleen
17	chr12:1137600-1164400	Weak transcription	Gastric	stomach
18	chr12:1137600-1172200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:1137800-1150800	Weak transcription	Thymus	Thymus
20	chr12:1137800-1152600	Weak transcription	NHEK	skin
21	chr12:1137800-1153200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:1137800-1153200	Weak transcription	HepG2	liver
23	chr12:1137800-1153200	Weak transcription	Osteobl	bone
24	chr12:1137800-1155800	Weak transcription	Left Ventricle	heart
25	chr12:1137800-1157200	Weak transcription	Ovary	ovary
26	chr12:1137800-1157200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr12:1137800-1162800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr12:1137800-1167400	Weak transcription	Lung	lung
29	chr12:1137800-1172200	Weak transcription	Aorta	Aorta
30	chr12:1138000-1149400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr12:1138000-1151000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr12:1138000-1151200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:1138000-1153200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:1138000-1157000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:1138000-1157200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr12:1138000-1157200	Weak transcription	Fetal Muscle Leg	muscle
37	chr12:1138000-1166600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr12:1138000-1172200	Weak transcription	Placenta	Placenta
39	chr12:1138200-1164200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr12:1138400-1163000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr12:1138600-1160400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:1138600-1167000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:1138800-1153200	Weak transcription	Hela-S3	cervix
44	chr12:1138800-1153200	Weak transcription	NH-A	brain
45	chr12:1138800-1163000	Weak transcription	Fetal Intestine Large	intestine
46	chr12:1139000-1150800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:1139000-1152800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr12:1139000-1153200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr12:1139800-1148200	Weak transcription	Brain Anterior Caudate	brain
50	chr12:1139800-1150600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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