Variant report

Variant	rs3768396
Chromosome Location	chr1:226884293-226884294
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:226884166..226888758-chr1:226889043..226894194,11	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1070361	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1071530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1288936	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1288938	0.93[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1288939	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3768393	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3820640	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs697847	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs708766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][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	nsv522446	chr1:226785530-226923938	Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv997468	chr1:226858660-226975311	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv535316	chr1:226858660-226975311	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226868200-226884600	Enhancers	Brain Substantia Nigra	brain
2	chr1:226868600-226884800	Weak transcription	Fetal Kidney	kidney
3	chr1:226868600-226888200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:226869000-226884400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:226870000-226888800	Genic enhancers	Primary T cells fromperipheralblood	blood
6	chr1:226872800-226890000	Weak transcription	Pancreas	Pancrea
7	chr1:226873400-226884600	Weak transcription	Gastric	stomach
8	chr1:226874400-226885200	Weak transcription	Colonic Mucosa	Colon
9	chr1:226875200-226884600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:226876600-226884400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:226876600-226885000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:226876800-226884800	Weak transcription	HSMM	muscle
13	chr1:226876800-226887600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr1:226876800-226890400	Genic enhancers	Primary T cells from cord blood	blood
15	chr1:226877200-226884600	Weak transcription	NHDF-Ad	bronchial
16	chr1:226877800-226890200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr1:226878400-226890800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:226878600-226889400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:226878600-226889600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:226879000-226886600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:226879200-226885000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:226879200-226890800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:226879800-226884400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
24	chr1:226879800-226890200	Weak transcription	Fetal Intestine Large	intestine
25	chr1:226880000-226884600	Weak transcription	NH-A	brain
26	chr1:226880200-226885200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr1:226880200-226888800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
28	chr1:226880200-226888800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr1:226880400-226886000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:226880800-226884400	Weak transcription	Small Intestine	intestine
31	chr1:226880800-226884800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr1:226880800-226888800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:226881000-226884400	Enhancers	Stomach Smooth Muscle	stomach
34	chr1:226881000-226884400	Strong transcription	Thymus	Thymus
35	chr1:226881000-226885600	Weak transcription	Lung	lung
36	chr1:226881000-226889600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:226881200-226884400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:226881200-226884400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr1:226881200-226884400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:226881200-226884800	Weak transcription	Fetal Lung	lung
41	chr1:226881200-226885200	Weak transcription	Placenta	Placenta
42	chr1:226881200-226890600	Weak transcription	Aorta	Aorta
43	chr1:226881600-226888600	Genic enhancers	Primary B cells from cord blood	blood
44	chr1:226881800-226884800	Enhancers	Brain Cingulate Gyrus	brain
45	chr1:226882200-226886800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:226882400-226884400	Enhancers	Adipose Nuclei	Adipose
47	chr1:226882400-226886000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:226882400-226887200	Enhancers	Brain Angular Gyrus	brain
49	chr1:226882400-226890200	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr1:226882400-226890600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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