Variant report

Variant	rs61946067
Chromosome Location	chr12:118740957-118740958
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:118740466..118742711-chr12:118813102..118814672,2	MCF-7	breast:
2	chr12:118735634..118738198-chr12:118739744..118741334,2	K562	blood:
3	chr12:118728193..118730845-chr12:118739160..118741836,2	K562	blood:

Variant related genes	Relation type
ENSG00000270482	Chromatin interaction
ENSG00000111707	Chromatin interaction

Extended variants
information (count: 171 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:167)

rs_ID	r²[population]
rs10507286	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11068891	0.83[EUR][1000 genomes]
rs11068906	0.88[EUR][1000 genomes]
rs11068908	0.87[EUR][1000 genomes]
rs11068910	0.83[EUR][1000 genomes]
rs12229607	0.87[EUR][1000 genomes]
rs12308475	0.82[EUR][1000 genomes]
rs16948193	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16948197	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16948204	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16948230	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16948234	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17433217	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17440364	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17440433	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17440669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17440774	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17440823	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17440893	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17440942	0.91[AFR][1000 genomes]
rs17441033	0.82[AFR][1000 genomes]
rs17441047	0.82[AFR][1000 genomes]
rs17441075	0.82[AFR][1000 genomes]
rs17441172	0.91[AFR][1000 genomes]
rs17441251	0.91[AFR][1000 genomes]
rs17512142	0.82[AMR][1000 genomes]
rs17512177	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17512198	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17512219	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17512407	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17512483	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17512525	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17512574	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17512609	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17512644	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17512652	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17512763	0.82[AFR][1000 genomes]
rs17513006	0.91[AFR][1000 genomes]
rs17513013	0.91[AFR][1000 genomes]
rs1909617	1.00[AFR][1000 genomes]
rs2055534	0.82[AFR][1000 genomes]
rs2393403	0.91[AFR][1000 genomes]
rs2393415	0.91[AFR][1000 genomes]
rs2393416	0.91[AFR][1000 genomes]
rs2784	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3852531	0.91[AFR][1000 genomes]
rs3852532	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4406856	0.91[AFR][1000 genomes]
rs4457791	0.91[AFR][1000 genomes]
rs4766900	0.81[EUR][1000 genomes]
rs4767669	0.82[AFR][1000 genomes]
rs4767670	0.82[AFR][1000 genomes]
rs4767672	0.91[AFR][1000 genomes]
rs55833534	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55842338	0.91[AFR][1000 genomes]
rs56033674	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56133316	0.82[AFR][1000 genomes]
rs56284927	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs56347775	0.91[AFR][1000 genomes]
rs56708462	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58113338	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58884645	0.83[EUR][1000 genomes]
rs61943362	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943364	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943365	0.85[EUR][1000 genomes]
rs61943367	1.00[AFR][1000 genomes]
rs61943368	1.00[AFR][1000 genomes]
rs61943385	1.00[AFR][1000 genomes]
rs61943389	0.91[AFR][1000 genomes]
rs61943392	0.91[AFR][1000 genomes]
rs61943393	0.82[AFR][1000 genomes]
rs61943397	0.81[EUR][1000 genomes]
rs61943399	0.82[AFR][1000 genomes]
rs61943400	0.91[AFR][1000 genomes]
rs61943401	0.82[AFR][1000 genomes]
rs61943402	0.82[AFR][1000 genomes]
rs61943403	0.81[EUR][1000 genomes]
rs61943404	0.82[AFR][1000 genomes]
rs61943406	0.82[AFR][1000 genomes]
rs61943443	0.82[AFR][1000 genomes]
rs61943444	0.91[AFR][1000 genomes]
rs61943447	0.91[AFR][1000 genomes]
rs61943451	0.91[AFR][1000 genomes]
rs61943452	0.91[AFR][1000 genomes]
rs61943454	0.91[AFR][1000 genomes]
rs61943455	0.91[AFR][1000 genomes]
rs61943456	0.91[AFR][1000 genomes]
rs61943457	0.91[AFR][1000 genomes]
rs61943535	0.81[EUR][1000 genomes]
rs61943538	0.81[EUR][1000 genomes]
rs61945175	0.80[EUR][1000 genomes]
rs61945176	0.80[EUR][1000 genomes]
rs61945177	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61945180	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61945181	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61945182	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61945183	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61945184	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61945187	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61945188	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61945189	0.91[AFR][1000 genomes]
rs61945190	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61945192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61945206	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61945210	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61945212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61945216	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61945217	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61945218	0.90[EUR][1000 genomes]
rs61945219	0.83[EUR][1000 genomes]
rs61945220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61945221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61945223	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945224	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945225	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945226	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945228	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61946063	0.82[EUR][1000 genomes]
rs61946064	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61946068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs673078	0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7132753	0.91[AFR][1000 genomes]
rs7136676	0.82[AFR][1000 genomes]
rs7137055	0.82[AFR][1000 genomes]
rs7137184	0.91[AFR][1000 genomes]
rs7294498	0.85[EUR][1000 genomes]
rs7299040	0.91[AFR][1000 genomes]
rs7302387	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303417	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7304342	0.81[EUR][1000 genomes]
rs7305647	0.82[AFR][1000 genomes]
rs7307393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309484	0.82[AFR][1000 genomes]
rs7309671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7314987	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73205512	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73205526	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73205531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73205551	0.82[EUR][1000 genomes]
rs73205553	1.00[ASN][1000 genomes]
rs73205576	0.91[AFR][1000 genomes]
rs73205594	0.91[AFR][1000 genomes]
rs73207504	0.91[AFR][1000 genomes]
rs73207564	0.91[AFR][1000 genomes]
rs73207566	0.91[AFR][1000 genomes]
rs73222058	0.83[EUR][1000 genomes]
rs7954330	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7957828	0.82[EUR][1000 genomes]
rs7958551	0.91[AFR][1000 genomes]
rs7958652	0.91[AFR][1000 genomes]
rs7960802	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7961312	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962185	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963353	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7963464	0.83[EUR][1000 genomes]
rs7965350	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7967900	0.82[AFR][1000 genomes]
rs7968011	0.91[AFR][1000 genomes]
rs7970481	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7973455	0.91[AMR][1000 genomes]
rs7974718	0.83[EUR][1000 genomes]
rs7977403	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs884844	0.80[EUR][1000 genomes]
rs950288	0.82[AFR][1000 genomes]
rs965524	0.82[AFR][1000 genomes]
rs9669004	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943819	0.83[EUR][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	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1038224	chr12:118648415-118791388	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1040061	chr12:118648415-118800437	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1053417	chr12:118688969-118808530	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118676000-118745200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr12:118693400-118745000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:118702600-118744600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr12:118712400-118745000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:118715000-118741200	Weak transcription	Thymus	Thymus
6	chr12:118719200-118744400	Weak transcription	HSMM	muscle
7	chr12:118720800-118793600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:118722600-118745000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:118726600-118746800	Weak transcription	Lung	lung
10	chr12:118728400-118744400	Weak transcription	NHLF	lung
11	chr12:118731200-118744400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:118732600-118744800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:118732800-118767600	Weak transcription	Primary T cells from cord blood	blood
14	chr12:118733400-118745000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr12:118735000-118744600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr12:118735400-118744400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr12:118735600-118745000	Weak transcription	Primary B cells from cord blood	blood
18	chr12:118736200-118746000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr12:118736600-118742600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:118737600-118741200	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr12:118738000-118742000	Enhancers	NHEK	skin
22	chr12:118738000-118744600	Weak transcription	Fetal Intestine Small	intestine
23	chr12:118738000-118745000	Weak transcription	Small Intestine	intestine
24	chr12:118738200-118741200	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr12:118738200-118744400	Weak transcription	NH-A	brain
26	chr12:118738200-118745200	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:118738200-118761800	Weak transcription	Fetal Lung	lung
28	chr12:118738400-118741200	Weak transcription	Brain Substantia Nigra	brain
29	chr12:118738400-118744800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:118738400-118745000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:118738600-118745200	Weak transcription	Brain Anterior Caudate	brain
32	chr12:118738600-118745600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr12:118738800-118741600	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr12:118739000-118741800	Enhancers	NHDF-Ad	bronchial
35	chr12:118739000-118744800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr12:118739200-118741000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:118739200-118749400	Weak transcription	Brain Angular Gyrus	brain
38	chr12:118739400-118743000	Enhancers	GM12878-XiMat	blood
39	chr12:118739600-118741000	Enhancers	Hela-S3	cervix
40	chr12:118739600-118741200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:118739600-118741400	Enhancers	HMEC	breast
42	chr12:118739800-118741400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr12:118740000-118741200	Enhancers	Primary hematopoietic stem cells	blood
44	chr12:118740000-118741200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:118740000-118745000	Weak transcription	K562	blood
46	chr12:118740200-118742400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:118740200-118744600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:118740200-118744800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr12:118740200-118745000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:118740200-118745000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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