Variant report

Variant	rs12196468
Chromosome Location	chr6:149454175-149454176
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149399566..149401649-chr6:149452459..149454867,2	MCF-7	breast:
2	chr6:149440091..149442908-chr6:149453590..149455859,2	K562	blood:
3	chr6:149352345..149354337-chr6:149453451..149455429,2	MCF-7	breast:
4	chr6:149449802..149452277-chr6:149452682..149455002,2	K562	blood:
5	chr6:149452280..149455428-chr6:149458542..149462690,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236591	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11155625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11756915	0.97[EUR][1000 genomes]
rs12191264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191441	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12196841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198786	0.97[EUR][1000 genomes]
rs12200486	0.96[EUR][1000 genomes]
rs12210293	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212173	0.96[EUR][1000 genomes]
rs12212622	0.96[EUR][1000 genomes]
rs12216302	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069314	0.97[EUR][1000 genomes]
rs28641142	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35030564	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35372633	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35426452	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3934770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935038	0.97[EUR][1000 genomes]
rs4243485	0.97[EUR][1000 genomes]
rs4243486	0.97[EUR][1000 genomes]
rs4283906	0.97[EUR][1000 genomes]
rs4355632	0.97[EUR][1000 genomes]
rs4385337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4415179	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4495293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4544932	0.97[EUR][1000 genomes]
rs4624897	0.97[EUR][1000 genomes]
rs4895779	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4897081	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4897082	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4897083	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4897084	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4897087	0.97[EUR][1000 genomes]
rs5013008	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55794530	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55855829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55953746	0.97[EUR][1000 genomes]
rs55991942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56260426	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56328446	0.97[EUR][1000 genomes]
rs56396328	0.97[EUR][1000 genomes]
rs56883363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56924759	0.97[EUR][1000 genomes]
rs57292049	0.98[EUR][1000 genomes]
rs57478974	0.97[EUR][1000 genomes]
rs57596511	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57937779	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58571272	0.97[EUR][1000 genomes]
rs61228112	0.97[EUR][1000 genomes]
rs61462811	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61660880	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62425896	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6570941	0.84[AMR][1000 genomes]
rs6570942	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6570943	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6909824	0.97[EUR][1000 genomes]
rs6934263	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7741894	0.97[EUR][1000 genomes]
rs7743161	0.96[EUR][1000 genomes]
rs7749723	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7749728	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7767040	0.92[EUR][1000 genomes]
rs9377192	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9386246	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9390658	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9688704	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9766171	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1024776	chr6:149398652-149654593	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149447600-149454400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr6:149447800-149454200	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr6:149448800-149454200	Enhancers	Placenta	Placenta
4	chr6:149449800-149454200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr6:149449800-149455600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:149450000-149454400	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr6:149450000-149457000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:149450000-149461200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:149450200-149455800	Enhancers	K562	blood
10	chr6:149450200-149461200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:149451600-149455800	Weak transcription	Fetal Kidney	kidney
12	chr6:149451800-149455800	Weak transcription	Adipose Nuclei	Adipose
13	chr6:149452000-149455000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:149452000-149458000	Weak transcription	Pancreas	Pancrea
15	chr6:149452200-149455000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:149452400-149454400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:149452600-149454200	Enhancers	Gastric	stomach
18	chr6:149452600-149454600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:149452600-149454800	Weak transcription	Fetal Lung	lung
20	chr6:149453000-149454200	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr6:149453000-149454200	Enhancers	Stomach Mucosa	stomach
22	chr6:149453000-149454400	Enhancers	Primary T cells from cord blood	blood
23	chr6:149453200-149454200	Enhancers	Primary T cells fromperipheralblood	blood
24	chr6:149453400-149454200	Enhancers	GM12878-XiMat	blood
25	chr6:149453600-149454200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:149453600-149454200	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr6:149453600-149454200	Enhancers	Spleen	Spleen
28	chr6:149453600-149454200	Enhancers	Dnd41	blood
29	chr6:149453600-149455800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:149453800-149454200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:149453800-149454400	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr6:149454000-149454200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:149454000-149454200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr6:149454000-149454200	Enhancers	Fetal Thymus	thymus
35	chr6:149454000-149454400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:149454000-149457200	Enhancers	Primary hematopoietic stem cells	blood
37	chr6:149454000-149459200	Weak transcription	Esophagus	oesophagus

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