Variant report

Variant	rs2229237
Chromosome Location	chr1:154401796-154401797
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154401123..154404227-chr1:154404483..154407452,3	MCF-7	breast:
2	chr1:154378359..154380579-chr1:154401148..154402901,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228013	Chromatin interaction
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11265614	1.00[EUR][1000 genomes]
rs35938325	1.00[EUR][1000 genomes]
rs41308415	1.00[EUR][1000 genomes]
rs41310931	0.89[EUR][1000 genomes]
rs57342848	1.00[EUR][1000 genomes]
rs58229059	1.00[EUR][1000 genomes]
rs58281895	1.00[EUR][1000 genomes]
rs59502179	1.00[EUR][1000 genomes]
rs73014267	1.00[EUR][1000 genomes]
rs73014271	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73014279	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73016210	1.00[EUR][1000 genomes]
rs73026642	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154383000-154402800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:154389000-154402800	Enhancers	Stomach Mucosa	stomach
3	chr1:154392800-154402800	Weak transcription	Fetal Brain Male	brain
4	chr1:154393000-154405800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr1:154393600-154402800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:154393800-154402600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:154393800-154403600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:154394000-154404000	Weak transcription	GM12878-XiMat	blood
9	chr1:154396800-154402200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:154397000-154402200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:154397000-154402800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:154397000-154414200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:154397200-154402400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:154397200-154402600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:154397200-154403800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:154398400-154403400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:154399200-154402200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr1:154399400-154403200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:154399400-154405800	Enhancers	Right Atrium	heart
20	chr1:154399400-154407200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:154399600-154401800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:154399600-154401800	Enhancers	Esophagus	oesophagus
23	chr1:154399600-154401800	Enhancers	Fetal Muscle Leg	muscle
24	chr1:154399600-154401800	Enhancers	Pancreas	Pancrea
25	chr1:154399600-154401800	Enhancers	Psoas Muscle	Psoas
26	chr1:154399600-154401800	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr1:154399600-154402000	Enhancers	Fetal Heart	heart
28	chr1:154399600-154402200	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr1:154399600-154402200	Enhancers	Left Ventricle	heart
30	chr1:154399600-154402600	Enhancers	Right Ventricle	heart
31	chr1:154399600-154402800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:154399600-154403000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr1:154399600-154403600	Enhancers	Fetal Intestine Small	intestine
34	chr1:154399600-154403800	Enhancers	Gastric	stomach
35	chr1:154399600-154404400	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr1:154399600-154404800	Enhancers	Brain Germinal Matrix	brain
37	chr1:154399600-154406800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:154399600-154409200	Enhancers	Placenta	Placenta
39	chr1:154399800-154401800	Enhancers	HSMMtube	muscle
40	chr1:154399800-154401800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr1:154399800-154402000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:154399800-154402400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:154399800-154402600	Enhancers	Brain Anterior Caudate	brain
44	chr1:154399800-154402600	Enhancers	Brain Hippocampus Middle	brain
45	chr1:154399800-154403000	Enhancers	Brain Cingulate Gyrus	brain
46	chr1:154399800-154404000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr1:154399800-154405600	Enhancers	Fetal Intestine Large	intestine
48	chr1:154399800-154405800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
49	chr1:154399800-154406200	Genic enhancers	Primary T cells fromperipheralblood	blood
50	chr1:154400000-154403200	Enhancers	Brain Angular Gyrus	brain

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