Variant report

Variant	rs3768397
Chromosome Location	chr1:226884501-226884502
allele	A/T
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:
2	chr1:226880953..226883068-chr1:226884444..226887006,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12095028	1.00[ASN][1000 genomes]
rs16846351	0.91[ASN][1000 genomes]
rs16846357	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16846378	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16846452	0.86[AMR][1000 genomes]
rs16846458	0.86[AMR][1000 genomes]
rs16846461	0.86[AMR][1000 genomes]
rs16846464	0.86[AMR][1000 genomes]
rs3754398	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754399	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754400	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754401	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754402	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754403	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754406	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754407	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754413	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3754417	0.83[AMR][1000 genomes]
rs3768388	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3768389	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3768400	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3768416	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3820641	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3820647	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4653461	1.00[ASN][1000 genomes]
rs4653464	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56095953	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs58091460	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7524854	0.93[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:100 , 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	chr1:226870000-226888800	Genic enhancers	Primary T cells fromperipheralblood	blood
5	chr1:226872800-226890000	Weak transcription	Pancreas	Pancrea
6	chr1:226873400-226884600	Weak transcription	Gastric	stomach
7	chr1:226874400-226885200	Weak transcription	Colonic Mucosa	Colon
8	chr1:226875200-226884600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:226876600-226885000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:226876800-226884800	Weak transcription	HSMM	muscle
11	chr1:226876800-226887600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr1:226876800-226890400	Genic enhancers	Primary T cells from cord blood	blood
13	chr1:226877200-226884600	Weak transcription	NHDF-Ad	bronchial
14	chr1:226877800-226890200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr1:226878400-226890800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:226878600-226889400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:226878600-226889600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:226879000-226886600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:226879200-226885000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:226879200-226890800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:226879800-226890200	Weak transcription	Fetal Intestine Large	intestine
22	chr1:226880000-226884600	Weak transcription	NH-A	brain
23	chr1:226880200-226885200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr1:226880200-226888800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
25	chr1:226880200-226888800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr1:226880400-226886000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:226880800-226884800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:226880800-226888800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:226881000-226885600	Weak transcription	Lung	lung
30	chr1:226881000-226889600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:226881200-226884800	Weak transcription	Fetal Lung	lung
32	chr1:226881200-226885200	Weak transcription	Placenta	Placenta
33	chr1:226881200-226890600	Weak transcription	Aorta	Aorta
34	chr1:226881600-226888600	Genic enhancers	Primary B cells from cord blood	blood
35	chr1:226881800-226884800	Enhancers	Brain Cingulate Gyrus	brain
36	chr1:226882200-226886800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:226882400-226886000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:226882400-226887200	Enhancers	Brain Angular Gyrus	brain
39	chr1:226882400-226890200	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr1:226882400-226890600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:226882800-226885000	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr1:226882800-226885800	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr1:226882800-226888600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:226883000-226884800	Enhancers	Brain Anterior Caudate	brain
45	chr1:226883000-226886200	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr1:226883000-226886800	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr1:226883200-226884800	Enhancers	Fetal Brain Male	brain
48	chr1:226883200-226886400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:226883200-226886400	Enhancers	Esophagus	oesophagus
50	chr1:226883200-226886600	Genic enhancers	Fetal Muscle Trunk	muscle

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