Variant report

Variant	rs17690541
Chromosome Location	chr2:127424389-127424390
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	chr2:127423618..127425430-chr2:127436236..127438617,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235128	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11692939	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13398914	0.82[JPT][hapmap]
rs17690564	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17741574	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28387109	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28387114	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs28387125	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28387126	0.95[ASN][1000 genomes]
rs28387130	0.83[ASN][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	nsv1002265	chr2:127029745-127733458	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv535919	chr2:127029745-127733458	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv583011	chr2:127386211-127489031	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv875001	chr2:127402833-127431312	Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv1813823	chr2:127417657-127441005	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127415200-127428000	Weak transcription	Gastric	stomach
2	chr2:127415600-127424600	Enhancers	Right Ventricle	heart
3	chr2:127416200-127429000	Weak transcription	Fetal Intestine Small	intestine
4	chr2:127416200-127430000	Weak transcription	Fetal Intestine Large	intestine
5	chr2:127416200-127430200	Weak transcription	Aorta	Aorta
6	chr2:127416600-127425000	Enhancers	Fetal Heart	heart
7	chr2:127416800-127425400	Weak transcription	Small Intestine	intestine
8	chr2:127417200-127425000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:127417200-127433000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:127417200-127443600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:127417600-127424600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:127417800-127426800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:127418000-127425400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:127419000-127426800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:127419400-127424600	Enhancers	Colon Smooth Muscle	Colon
16	chr2:127420200-127424600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr2:127420600-127424800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr2:127420600-127430400	Weak transcription	Fetal Lung	lung
19	chr2:127420800-127424600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:127421000-127424800	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr2:127421400-127424800	Enhancers	Left Ventricle	heart
22	chr2:127421400-127424800	Genic enhancers	K562	blood
23	chr2:127421400-127430200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:127421800-127424800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:127422200-127453400	Weak transcription	Colonic Mucosa	Colon
26	chr2:127422600-127424400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:127422600-127424400	Enhancers	Stomach Smooth Muscle	stomach
28	chr2:127422600-127424800	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr2:127422600-127425000	Enhancers	Primary T cells from cord blood	blood
30	chr2:127422600-127426000	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr2:127422600-127427000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr2:127422600-127427400	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr2:127422600-127427600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:127422800-127424800	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr2:127422800-127427800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr2:127423000-127424800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:127423000-127426400	Genic enhancers	Primary T cells fromperipheralblood	blood
38	chr2:127423200-127424600	Enhancers	Esophagus	oesophagus
39	chr2:127423200-127424800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:127423200-127426000	Enhancers	Ovary	ovary
41	chr2:127423200-127427800	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr2:127423400-127424600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:127423400-127424600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:127423400-127424600	Enhancers	Rectal Smooth Muscle	rectum
45	chr2:127423400-127424600	Enhancers	HSMM	muscle
46	chr2:127423400-127424800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr2:127423400-127424800	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr2:127423400-127424800	Enhancers	Spleen	Spleen
49	chr2:127423400-127424800	Enhancers	HSMMtube	muscle
50	chr2:127423600-127424400	Weak transcription	Primary B cells from cord blood	blood

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