Variant report

Variant	rs12404261
Chromosome Location	chr1:92213835-92213836
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:92198271..92200616-chr1:92212506..92214595,2	MCF-7	breast:
2	chr1:92207551..92212491-chr1:92212891..92216237,4	K562	blood:
3	chr1:92211221..92213860-chr1:92214321..92216295,2	K562	blood:
4	chr1:92195746..92200158-chr1:92212228..92214643,4	K562	blood:
5	chr1:92208195..92211012-chr1:92213162..92216237,4	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12404952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12406783	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17882046	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72716403	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers 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	33 gene(s)	inside rSNPs	diseases
3	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats 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
5	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription 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	19 gene(s)	inside rSNPs	diseases
6	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv1005917	chr1:92189945-92378683	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer 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	4 gene(s)	inside rSNPs	diseases
8	nsv949449	chr1:92211020-92585831	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92197000-92215200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:92197200-92215400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:92197600-92230000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:92198200-92224400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:92199200-92218600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:92199400-92219000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:92201200-92219000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:92201400-92217600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:92204800-92247000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:92208400-92235800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:92208800-92214800	Weak transcription	Brain Substantia Nigra	brain
12	chr1:92209200-92215600	Weak transcription	Osteobl	bone
13	chr1:92209200-92217000	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr1:92211000-92215200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:92211000-92215600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:92211200-92215000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:92211200-92215200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:92211200-92215800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:92211200-92216000	Weak transcription	Aorta	Aorta
20	chr1:92211400-92215400	Weak transcription	Small Intestine	intestine
21	chr1:92211400-92215800	Weak transcription	Brain Angular Gyrus	brain
22	chr1:92211600-92216200	Weak transcription	Brain Germinal Matrix	brain
23	chr1:92211800-92214800	Weak transcription	Brain Anterior Caudate	brain
24	chr1:92211800-92215400	Weak transcription	Pancreas	Pancrea
25	chr1:92211800-92215600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:92211800-92235600	Weak transcription	Fetal Kidney	kidney
27	chr1:92212000-92214000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:92212000-92214200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:92212000-92215000	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:92212000-92216800	Weak transcription	Fetal Heart	heart
31	chr1:92212600-92214000	Strong transcription	Fetal Stomach	stomach
32	chr1:92212600-92214000	Genic enhancers	Left Ventricle	heart
33	chr1:92212600-92214200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:92212600-92214800	Weak transcription	Right Atrium	heart
35	chr1:92212800-92215800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:92212800-92217600	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr1:92213000-92214600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:92213000-92214800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:92213000-92214800	Weak transcription	Lung	lung
40	chr1:92213000-92215200	Strong transcription	Fetal Muscle Trunk	muscle
41	chr1:92213000-92215200	Weak transcription	Placenta	Placenta
42	chr1:92213000-92215600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr1:92213000-92216200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr1:92213000-92216600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr1:92213000-92218000	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr1:92213000-92224000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:92213200-92214000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:92213200-92214200	Genic enhancers	Ovary	ovary
49	chr1:92213200-92214800	Strong transcription	Fetal Muscle Leg	muscle
50	chr1:92213200-92215000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland

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