Variant report

Variant	rs56284927
Chromosome Location	chr12:118790568-118790569
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:118573188..118576154-chr12:118790437..118793142,2	MCF-7	breast:
2	chr12:118789693..118801109-chr12:118805205..118813455,21	K562	blood:
3	chr12:118789460..118791189-chr12:118792284..118794787,2	K562	blood:

Variant related genes	Relation type
ENSG00000135090	Chromatin interaction
ENSG00000176834	Chromatin interaction
ENSG00000089220	Chromatin interaction

Extended variants
information (count: 176 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:172)

rs_ID	r²[population]
rs1060964	0.83[EUR][1000 genomes]
rs10850967	0.81[EUR][1000 genomes]
rs11068908	0.81[EUR][1000 genomes]
rs11068917	0.91[EUR][1000 genomes]
rs11068919	0.87[EUR][1000 genomes]
rs11068926	0.84[EUR][1000 genomes]
rs12229607	0.81[EUR][1000 genomes]
rs16948193	0.85[EUR][1000 genomes]
rs16948197	0.85[EUR][1000 genomes]
rs16948204	0.83[EUR][1000 genomes]
rs16948230	0.85[EUR][1000 genomes]
rs16948234	0.87[EUR][1000 genomes]
rs17433217	0.85[EUR][1000 genomes]
rs17440433	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17440669	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17440774	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17440823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17440893	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17440942	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17440956	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17441033	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17441047	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17441061	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17441075	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17441172	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs17441214	0.81[AMR][1000 genomes]
rs17441251	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs17512219	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17512407	0.91[AFR][1000 genomes]
rs17512483	0.91[AFR][1000 genomes]
rs17512525	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17512574	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17512609	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17512644	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17512652	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17512763	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17513006	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs17513013	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs17619932	0.92[EUR][1000 genomes]
rs1909617	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2036314	0.85[EUR][1000 genomes]
rs2036489	0.81[EUR][1000 genomes]
rs2055534	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2062519	0.81[EUR][1000 genomes]
rs2393403	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2393415	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2393416	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2784	0.91[AFR][1000 genomes]
rs3852531	0.91[AFR][1000 genomes]
rs3852532	0.85[EUR][1000 genomes]
rs4406856	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4442583	0.84[EUR][1000 genomes]
rs4457791	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4766899	0.81[EUR][1000 genomes]
rs4766900	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4767669	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4767670	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4767671	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4767672	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55659011	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55833534	0.87[EUR][1000 genomes]
rs55842338	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs55929628	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56033674	0.85[EUR][1000 genomes]
rs56133316	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56157623	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56275187	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56324376	0.81[EUR][1000 genomes]
rs56347775	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs56708462	0.87[EUR][1000 genomes]
rs58113338	0.85[EUR][1000 genomes]
rs59594854	0.81[EUR][1000 genomes]
rs61943362	0.91[AFR][1000 genomes]
rs61943364	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61943367	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61943368	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61943369	0.85[EUR][1000 genomes]
rs61943370	0.84[EUR][1000 genomes]
rs61943371	0.84[EUR][1000 genomes]
rs61943385	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61943388	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61943389	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61943391	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61943392	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61943393	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61943397	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61943399	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61943400	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61943401	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61943402	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61943403	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61943404	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61943405	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61943406	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61943443	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61943444	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61943447	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs61943451	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs61943452	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs61943454	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs61943455	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs61943456	0.91[AFR][1000 genomes]
rs61943457	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs61945180	0.81[EUR][1000 genomes]
rs61945181	0.81[EUR][1000 genomes]
rs61945182	0.85[EUR][1000 genomes]
rs61945183	0.85[EUR][1000 genomes]
rs61945184	0.85[EUR][1000 genomes]
rs61945187	0.85[EUR][1000 genomes]
rs61945188	0.85[EUR][1000 genomes]
rs61945189	0.91[AFR][1000 genomes]
rs61945190	0.82[EUR][1000 genomes]
rs61945192	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs61945206	0.85[EUR][1000 genomes]
rs61945210	0.83[EUR][1000 genomes]
rs61945212	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs61945216	0.85[EUR][1000 genomes]
rs61945217	0.91[AFR][1000 genomes]
rs61945218	0.83[EUR][1000 genomes]
rs61945220	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs61945221	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs61945223	0.91[AFR][1000 genomes]
rs61945224	0.91[AFR][1000 genomes]
rs61945225	0.91[AFR][1000 genomes]
rs61945226	0.85[EUR][1000 genomes]
rs61945228	0.87[EUR][1000 genomes]
rs61946067	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs61946068	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6490177	0.84[EUR][1000 genomes]
rs673078	0.91[AFR][1000 genomes]
rs7132753	0.91[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7136676	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7137055	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7137184	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7295288	0.80[EUR][1000 genomes]
rs7299040	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7302387	0.91[AFR][1000 genomes]
rs7303417	0.85[EUR][1000 genomes]
rs7304342	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7305647	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7307393	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7309484	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7309671	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7312555	0.81[AMR][1000 genomes]
rs7314987	0.91[AFR][1000 genomes]
rs73205512	0.85[EUR][1000 genomes]
rs73205526	0.85[EUR][1000 genomes]
rs73205531	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs73205553	0.81[AMR][1000 genomes]
rs73205576	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73205579	0.88[AMR][1000 genomes]
rs73205594	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73207504	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs73207564	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs73207566	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7954330	0.83[EUR][1000 genomes]
rs7958551	0.91[AFR][1000 genomes]
rs7958652	0.91[AFR][1000 genomes]
rs7960802	0.91[AFR][1000 genomes]
rs7961312	0.91[AFR][1000 genomes]
rs7962185	0.85[EUR][1000 genomes]
rs7963353	0.85[EUR][1000 genomes]
rs7965350	0.85[EUR][1000 genomes]
rs7967900	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7968011	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7970481	0.85[EUR][1000 genomes]
rs7977403	0.82[EUR][1000 genomes]
rs882927	0.84[EUR][1000 genomes]
rs884844	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs950288	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs965524	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9669004	0.85[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56284927	SUDS3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118720800-118793600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:118769200-118791000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:118774000-118792400	Weak transcription	Dnd41	blood
4	chr12:118775800-118792000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:118775800-118792600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr12:118776200-118792000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:118777000-118791000	Weak transcription	NHDF-Ad	bronchial
8	chr12:118781000-118793600	Weak transcription	NHEK	skin
9	chr12:118783400-118791000	Weak transcription	NHLF	lung
10	chr12:118783600-118792200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:118783600-118793000	Weak transcription	Osteobl	bone
12	chr12:118783600-118794400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr12:118784200-118793600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr12:118785000-118792600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:118785000-118794600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:118785400-118790600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr12:118785400-118790600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:118785400-118792200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:118785400-118793000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:118785400-118794600	Weak transcription	Aorta	Aorta
21	chr12:118785600-118791000	Weak transcription	Primary B cells from cord blood	blood
22	chr12:118786000-118790600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr12:118786000-118791000	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr12:118786000-118791200	Weak transcription	Brain Substantia Nigra	brain
25	chr12:118786000-118791400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:118786000-118793400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr12:118786000-118794400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr12:118786200-118791000	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr12:118786200-118791000	Weak transcription	Brain Angular Gyrus	brain
30	chr12:118786200-118791000	Weak transcription	K562	blood
31	chr12:118786200-118791200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:118786200-118791400	Weak transcription	A549	lung
33	chr12:118786200-118791600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr12:118786200-118793400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:118786200-118793400	Weak transcription	Stomach Mucosa	stomach
36	chr12:118786200-118793600	Weak transcription	Brain Hippocampus Middle	brain
37	chr12:118786200-118793600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr12:118786200-118793800	Weak transcription	Colon Smooth Muscle	Colon
39	chr12:118786600-118793800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr12:118786800-118791200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr12:118786800-118792000	Weak transcription	Fetal Intestine Small	intestine
42	chr12:118788200-118790800	Weak transcription	GM12878-XiMat	blood
43	chr12:118788400-118791000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr12:118789200-118793200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr12:118789200-118793600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:118789400-118791000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:118789400-118791200	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr12:118789400-118793200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:118789600-118793200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr12:118790400-118791000	Enhancers	Liver	Liver

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